Well, you have to first find out if there is really a Virtual file system or the files just are hidden.
In the first case you have to crack the system to see where the files are actually there.
For the second, you maybe can find some traces of the files in the disc TOC.
Anyway by a look at the DVD one of the above really apply to KHFM.
A font can be in any file and not only in tim(2) files.
I am not very experienced on PS2 hacking but I made some research before answering here.
First of all, I checked the files of KHFM and KH2FM:
As you see, you are missing the big GB files in KHFM but those files are always in company of a nice IDX file as you see in the right part of the pic.
So my guess is that you are missing only one big file named KINGDOM.IMG.
The first thing you have to do is a way to find that file on disc and then extract it or at least make it visible.
To where the file is, well, by a look at the LBA, I would say it's sure to say that it start somewhere after LBA 2478 and the size can be calculated from the image size and the visible size.
The keys for your files are probably inside KINGDOM.IDX but I can't tell you how they work but the KHFM and KH2FM IDXs look like they have the same structure.
What is an help if it not depresses you a bit??
Well when you get that big file in your hands, it's looking like you have to extract/decompress or decrypt it and I can assure you that you will get alot of file out of it (KH2.IMG contains 5000+ files).
Why i know this, because there is an extractor that maybe you can try to misuse when got the KINGDOM.IMG file in your hands. If you can't misuse it, you can at least try to contact the maker so that you can create your own:http://xeeynamo.blogspot.com/2011/07/kingdom-hearts-ii-final-mix.html#more
In general, PS2 executables are ELF and you got those PRX so if you are not lucky and you not find everything you need in the IDX/IMG file, you probably need extractors/decrypter or decompressors from the net.
Last but not least you will need a program to reinsert the hidden IMG file into the iso (depending on how you extracted it) so maybe Apache (if you modified the TOC to make the file visible) or probably need to program your own tool to reinsert it.