I'd like to play, but I have RRM/RWM installed, and I don't want to uninstall RWM. Is it ok if I play with RWM and just not use the RWM-only runewords? If I change the start folder to the d2 install location (it's the Runewords folder right now), will RRM still work?
If you have RWM installed you may still play but you may not use Bnet runewords. So you dont have to uninstall it just play the game thinking you dont even have RWM.
Is reroll of ancients with TP allowed?
Yes you can re-roll ancients because you have not completeed it yet. so yes you can.
Also, at what point should I turn down player level for Act Bosses? For example, at/before entrance to durance3, or after killing Bremm/Maffer/Wyand?
You should turn down your players either just before the act boss ( out side duriels area, catacombs level 4 for Andariel etc...) basically if you want to change your players settings for the end act boss just make sure it is done before you vs him/her.(THIS IS NOT A SET RULE, IT JUST MEANS THAT YOU MAY TURN DOWN YOUR PLAYERS SETTINGS BEFORE ACT BOSSES)
And one more question: no re-run of areas in Normal, does that mean that I either have to reach a WP without killing anything, or run from a WP to the next area without killing anything, between game sessions? Guess it does, but just want to be sure. Might present some problems with 'closed-off' areas like the Graveyard...
Good question basically you dont have to do that. If you get to lets say lost city way point and you stop playing it does not mean that you cannot kill anything before the next way point. The rule was placed so people dont re-run pindle, pits ,WSK, act bosses etc. So to answer your question it is no you dont have to.
hope no one minds my playing with RWM installed
It is perfectly alright if it is installed as long as you dont use it. (example makings spirt, or in other words Bnet runewords)