Eh, it hasn't caused me enough trouble to worry about it, and again - in case of emergency I have NAND dumps and moderate soldering skills ready to do a hard-mod if I have to. I used the pack I did because it includes patched/removed TWL/AGB_FIRM, whitelist and mset files. I was asking around earlier about the plausibility of just updating the two missing cias (9.2 homemenu and CVer) and I'll probably end up doing that.
My payload's named ropbinpayload_menuhax_USA11272_old3ds.bin. It works, just not 100% of the time; sometimes it hangs on the yellow screen. I'd love to have a more stable version, but it's not the end of the world - for some reason the old (1.0/1.2) Themehax versions don't seem to run properly for me anymore; they show text for a split second, then go all garbled. I suspect incompatibilities with using *hax 2.5 to run them when they were build on 2.1; I know I've had them working before (on the same frankenfirmware setup).
Once you replace the payload, you aren't running anything of *hax 2.5 anymore.
Anyway 9.0 payloads are identical to 9.1 payloads. Think you'd be able to make a recording or something or what happens when you try running themehax 1.2/1.3, that you installed via the offline themehax 1.2/1.3 installers? (Either should work, because they both give you the same ropbin payload in the end and you uninstall it after you got the payload anyway. All you're really interested in is the ropbin payload for *hax 2.1)
Otherwise honestly get the full proper 9.2 update pack instead of the modified update pack, nothing to lose from it really. You will be on a clean 9.2 install and then my payload that I linked -should- work.
I wouldn't update "just the missing .cias", because honestly you don't know exactly which ones might be missing. Better to do a full update with the actual 9.2 pack, that way you know you aren't missing anything and you know you have all the proper system titles for 9.2
Then if you want, afterwards you can go back and install bluecardfix to rollback the whitelist, and downgrade sysnand system settings back to 4.x or 6.x if you care about mset entry point. But honestly should just keep the 9.x one anyway since you'll be using menuhax, and if menuhax ever stops working you have browserhax.
AGB_FIRM you don't need to have modified so you can have the clean one from the full update pack, rxTools auto-patches it on the fly when you run GBA games since a certain nightly (I use 9/28 nightly and it works.) Not sure about TWL_FIRM but every DS/i mode thing I throw at it works and I used full 9.2 update pack.
You could try deleting all the payloads from the otherapp payload directory in themehax_installer apart from the 9.0/9.1/9.2 ones, and the N3DS ones. You'll never need any of them.
Then make a copy of your 9.0/9.1 payload in that directory which are POST5_U_11272_8203.bin, rename it to POST5_U_12288_8203.bin and put it in place of the 9.2 payload. That way, you know that even if themehax installer recognizes your 3DS as 9.2 somehow then it will load a 9.0/9.1 payload anyway since you replaced them.