I think you've found some bad information or misunderstood something along the way.
To play a Xbox game from anything other than the original disc the Xbox must be either chipped, TSOPed or softmodded.
Any problems with specific games is usually due to the Xbox v1.6 Xcalibur video chip it uses. Rocky5's previously mentioned 480p v1.6 launcher XBMC script addresses that problem. There are a few games for which no launcher seems to work but all that means is that it will have to be played at 480i ie. it can still be played.
There are a few genuinely regional locked games too where the PAL version won't play on a NTSC/NSTC region changed Xbox or visa versa. That means some PAL versions are not playable in 480p because that option is a NTSC Xbox exclusive feature.
HDD Ready probably just means it has been ACL (Action Control List)* patched and, if necessary, includes the v1.6 patch too.
If it is provided as the game files, generally intended for FTPing to to the Xbox there is nothing to stop you making a XISO from them instead. You just need either Qwix or C-Xbox Tools, PC programs that are specifically designed to do that amongst other things. That XISO can then be burned (ImgBurn recommended) on DVD-R media and can be played from the disc or installed using DVD2Xbox as described.
There might be a problem with some games which include an already ACL patched "default.xbe" if you want to play the game from the burned disc
. I've never tried that but if it is a problem that "default.xbe_org" is the original game "default.xbe" so all you'd have to do is backup/rename the patched default.xbe and rename the original one back to "default.xbe", create a new XISO and burn the disc again.
Any issue like that are not connected with whether the Xbox is chipped,TSOPed or softmodded.
The problems you described are likely non-issues. If the files you have are from an original Xbox game disc the game should play just as well as it did originally. The only issues are those I've mentioned which are specific either to the v1.6 or regional. The patches described fix any display problems most of the time and AFAIK do not introduce any new ones.
DLC is added to those games, as said, once installed, as game save data (TDATA folder). Without testing particular DLC I do not know and doubt anyone one else her will know if there are specific problems with any DLC if the game is being played from a burned disc or install on the HDD. However as both have to access the same UDATA/TDATA game save folders created on the HDD when you first run a game by any method as long as there are no regional differences in those files' ID I can not see any reason why HDD installed or played from disc would make any difference.
The DLC installer I mentioned includes both extra DLC and game update DLC too. I've had a look at it and Doom 3 has no game update but there is a 16MB DLC installer package. A guide is included in that which is pretty self-explanatory.
I think I've found the place you download the files from and I'm currently downloading to test them myself.
Doom 3 is marked with a ! and I assume that is because there are comments from other downloaders which say it is graphically corrupt and unplayable. Sound familiar?
I might be wrong but I suspect they just need DVD2Xbox ACL patching but could be a regional problem too as I believe the source is Polish so they'll likely be PAL.
I finished downloading from the HDD ready place and its fine.
The folder you see with the '7' is a 7Zip folder not a 7GB one.
If you've not come across 7Zip it is 'simply' another file compression format type like ZIP or RAR. Its is very popular, particularly in gaming circles because it is considered to do a better job than ZIP and has more inbuilt options. I recommend you install it or an alternative which can open 7Zip folders instead of relying on your Windows tools. PeaZip and a whole slew of others can do that but it makes more sense to use the original 7Zip, IMHO.
The Doom 3 7Zip folder is actually only just over 2GB and decompressed under 3GB. Once 7Zip has done its job you should end up with an ordinary folder named "Doom 3". Inside that are all the normal game files you would expect.
To burn it to disc you need to create the XISO from that folder so find Qwix 101 or C-Xbox Tools v2.7 and use that to create the XISO. If you need help using it ask.
Once created launch ImgBurn > "Write image file to disc", browser to the Doom 3 folder and burn it at x4 speed or whatever is the lowest speed the media you're using supports (usually that is x4). It must be on DVD-R to guarantee compatibility with all Xbox disc drives but if you have DVD+R and you don't mind risking a wasted disc you can try that as the next most compatible type.
When burned fire up your Xbox and away you go.
I actually used DVD-RW which my Hitachi disc drive likes so I didn't have to waste any disc media on this either.
As far as I've tested it:-
1). The game plays perfectly from disc on a NTSC set PAL v1.6 chipped Xbox (480p Component cable)
2). Installed from that disc using DVD2Xbox - likewise plays perfectly from the ACL patched default.xbe and the original.
default.xbe_org when renamed. That suggest whatever the reported problem was it was not because it had not
been ACL patched.
I have no good reason to think playing it on a softmod instead would produce any different result but I will do that later. Installing the Doom 3 folder by FTP instead of via a disc seems pointless to test because the game files are clearly OK.
I'd bet now, knowing that they're good, it was FTPing that caused the problems for the other users. There are always troublesome files that won't FTP first time with any biggish file transfer to the Xbox. I'd guess one or more files did not FTP and they did not think to check let alone re-queue and try them again.
As for the DLC - I installed that too. It is just two multiplayer maps "Surface" and "Communications" installed in TDATA/41560020/$c.
Hope this info helps.
Just finished testing the disc on a softmod - SID 5 updated later by AID. Xbox v1.1.
From disc or HDD installed, patched or not all works and plays fine. The Samsung 605B disc drive initially had problems reading the DVD-RW (as expected) but eventually, and to my surprise, the game played perfectly from the disc and I could also use DVD2Xbox to install it to the HDD without any read problems too.
In short: the Doom 3 download you found is absolutely fine.