There are many limits in the Ghost Boot Wizard, some of which are more complex than the KB article linked above acknowledges. However, the basic problem is that the Ghost Boot Wizard in GSS 2.5, as in earlier versions, comes from code which only writes a basic ISO 9660 Level 1 filesystem; it's that specification which has MS-DOS style limits of 11 uppercase ASCII filename characters and limits the size of an individual file to 2Gb.
Of course, all of this can be (and was, at the cost of rewriting the entire optical drive subsystem of GBW and Ghost from the ground up) overcome, but being a ground-up rewrite it wasn't something that could just be dropped into the GSS 2.5 code line without consequences.
The end result is that although in principle these limits shouldn't exist (and there's code around which doesn't have them), it's not something that GSS 2.5 is likely to ever support - it's likely to be more of a 3.0 thing, and unless a 3.0 version is (re-)announced I wouldn't expect a solution to this.
A more complex issue along this line, since the original post mentions plain GHOST.EXE, i.e. the DOS executable, is that if you boot the DOS version of Ghost then if you use MSCDEX.EXE to access the CD you're stuck with the ISO 9660 Level 1 limits. As it happens, GHOST.EXE has its own direct CD reading code, but that too was limited to ISO 9660 Level 1 just as the writing code was (and had a collection of other really strange quirks). This means that in the context of DOS, even if you were to use a tool which would *write* ISO 9660 level 3 filesystems, there's no way the DOS-based Ghost.exe could read them, you would need to use WinPE or Linux.