So close, it wasn't the php.ini file issue, it was that the upgrade of phptools changed the php runtime engine it was referring to. I had to reset it to the PHP I had installed and the same one IIS was pointing to (as it worked in IIS, but not in phptools, I just didn't realize where VS was getting this setting from. Update the settings. (Alas, I have no CLI tab in mine, it was under settings in my case), and it was server /runtime which was incorrect.
Consider it fixed.