Yes, you can just pop in the trapdoor RAM and Super Denise and still yield great compatibility. Only a handful of games took advantage of the extra Chip RAM anyway. If you're working with graphics and sound however, you'll want to do the Chip RAM mod eventually and get yourself some Fast RAM for the side expansion port.
Only really old (like software written during the OS1.0/1.1 time) or poorly written software will "break" with the addition of Chip RAM, so I wouldn't worry about it.