I am currently in the middle of updating and reinstalling some mods including FNIS, but when I run it through MO it always generates the files in the "overwrite" folder for me. I'm not sure about the game crashing but what I did with the previous version was make sure my "overwrite" folder was empty, then run FNIS, and then create a mod from that (call it FNIS output or something) and then activate it in MO. I have followed a few guides that have mentioned this and so far it has worked for me. My game has a bunch of things I'm trying to fix so far I haven't had the "T-Pose" issue for awhile but another thing you could try is just rerunning FNIS before starting the game each time (I hope this isn't bad advice sorry if it is). Also make sure to tick or not tick the patches that you need in the tool itself (I'm just mentioning this because I have forgotten to do this a few times but only when I was rushing not paying attention). I hope this helps you and if not you might check the S.T.E.P. Wiki it might be a little more helpful than I am.