I'm a bit tired and just back from work...i see that u had some success...good.
First of all i confirm what Gemini said about the directory deeps. There are many games that use more than one directory deep...just see the pic of Metal Slug X:
I was just playing around to see if there is an easy way that u can get that extra directory to work and i discovered somethings that maybe can be helping u.
I was remembering there was a tool to build psx cd images so i tried to rip and rebuild VS with that tool but he gave me many times the error that the PSX supports max 30 files/directory (in fact it's wrong because we have many more files in each directory of VS)...umm
Ok, check my friend google and find out that that UltraIso can add directories and file to an ISO...ok, let's try it. just by adding an empty directory to the image of VS make ePSXe crash with error:
I had my Metal Slug X in the drive and decided to make the same with it because it's smaller...suprise... it works even with the XTRA directory and even with more files on that directory.
So, I don't remember exactly where all the differences between the different modes and image types are (longtime i don't fight with them heheh) but I would look what is the form of a TOC in a CD with less than xx files/directories (1350 files??) and the form of the TOC with more files/directories.
I rememeber something about a Secondary Descriptor, with less than xx files/directories u don't need the secondary descriptor ( u are probably modifying this version of TOC) and with more files u have to use it but it change the primary descriptor form too (I'm just remembering something like this). For this u will probably need to forget about the "rules" for the PSX and look on the iso9660 format.
Don't forget that u have 5132 files in 15 directories in VS and all need a place in the TOC (so much for the 45 directories*30files=1350...maybe in a standart PSX CD but not in this one heheh). Metal Slug X has 354 files in 28 directories.
By the way...why u want to add that directory??
I hope I could point to the right direction