Does nobody know of any other tools I could use? I have no idea what the hell Tinke is doing but it keeps corrupting the sdat once I modify and repack the SWAR folder inside it with Sonic's voice clips.
There are not many tools aimed at rebuilding or inserting.
It is pretty much tinke, vgmtrans (make sure to get the new fork), possibly MKDS course modifier and maybe crystaltile2 that have abilities with noting in all this (not played with Nitro Studio but you reckon it). A few others like vgmtoolbox to generate the SMAP files can be handy, as might any that extract files and display data. Most other tools are aimed at playback, extraction and conversion to common formats. There are some older tools as well (I think Tahaxan got a few things, kiwi.ds (guy that wrote up the first main SDAT spec) had a tool which tried to rebuild, I think lowline's console tool had a bit and there are a handful of others but most of those are even more broken than the ones mentioned before or that you are already using.
As mentioned I normally go manual and insert the files myself with a hex editor or something*, and also correct any settings the header might display. I will guide this editing with another tool that tells me where things are but it is still manual. I do this mainly as all the tools mentioned have an endless list of quirks and oddities where going manual takes longer but I know exactly what happened to get there.
*hopefully it is smaller and you can pad it out to match size, otherwise you repoint everything following it or maybe shuffle it to the end (don't recall the full SWAR format right now and if it can do that, works for other aspects though), expand the file and change the pointer for that one file to the end. If you are lucky there might be a redundant sound in there that is not used (I think it was one of the Castlevania games which still had the E3 trailer voiceover buried within it) and thus can be overwritten without troubling the final game if you do need more space.
As far as emulators go it is still a piece of code pretending to act like hardware, running a game that manages the interactions with that hardware. The emulation might be inaccurate (doubt it here if it plays the original games fine, not to mention you presumably still want the hack to work with an emulator) and introduce its own problems but for the most part treat it like it is hardware.