Just wondering what the policy is on this? If my run fits into a few different categories, can I submit it for each of those categories or should I do a separate run/video per category?

There is no site-wide policy for this. Each game has different rules, so check in the forums of the relevant game you play, or contact the game moderators directly about it.

Yup. Personally, I think a 100% run or a glitchless run or whatever absolutely can be an any% run. You should have a reason for submitting to both categories (i.e. - and yes this has actually happened - it's rekky for both categories). If any% is 20 minutes and 100% or glitchless are 4 hours, maybe don't submit that to the any% category? But it definitely shouldn't be blanket disallowed, even though same games do.