One question that popped right away was 4-player limit in multiplayer. Can someone tell me why is that and how easy would it be to expand it to at least 8 players multiplayer limit ?
You can but the D3 engine has a really high server resources requirement compared to Quake1/2/3 engines. The biggest "problem" with D3 isn't what it can't do but what it can: physics, lighting, shadows, etc. are all synced with the server & clients. Other engines don't bother with that. I wouldn't suggest more then 4 players unless you get an ETQW/Brink style MP setup.
Another question if there is a limit for entities in Doom 3 ?
It's high but could be changed in the code, just like the other id engines (I want to say 16 or 32k, but it includes all particles, projecticles, etc)
Can we spawn level dynamically (models with collision hulls), in the void outside of the level made in DoomRadiant ?
It's already been done, can even be done via scripts. However, scripts need to sync over network and that makes it more difficult (by default D3 doesn't sync everything to save bandwidth).
Can we spawn lights dynamically ?
Via scripts/triggers, yes.
For ToM I'd say stay with Darkplaces, it seems to work very well. Plus it has the nice deferred lighting, that looks sweet.