For hotspots, the Group.Player option assumes the hotspot of your character sprite is located at the bottom-center (i.e. the Feet) to place the sprite on the Mask. However, you can modify the default hotspot position by editing the Mask object instead. So if your character sprite was setup to use the hotspot in the center of the player, you can simply place the hotspot of the mask object in the center. Be sure to also edit the "Crouch Down" animation slot in the Mask as well (and keep the gap as well, as the ceiling detector uses YTop to position itself!). If you're using a physics object (placed in Group.2), you'll typically keep that in the center so it can rotate properly. The other groups have no specific requirement for hotspots.
As far as group combos go, there are indeed a few things to note:
-Group.0 (Solid Object) and Group.1 (Jump-Thru Object) obviously can't work together since 0 overrides everything.
-Group.0 can also be a bit weird if you use it with Group.2 (Physics) since it can throw off the mask's slope detection (use Group.1 instead)
-Group.1 is the most versatile group, as it can be combo'd with Group.2, Group.3, and Group.4 (Moving Object)
-Group.2 automatically adds collisions to any physics objects in this group. Can be combo'd with Group.1 and Group.4. Wonky with Group.0
-Group.3 (Ladder Object) only works well with Group.1, which lets the mask stand on top of it. Any other group won't work well with it.
-Group.4 makes objects ride-able for the mask, but needs to be paired with Group.0 or Group.1 to actually work.
-Group.5 (Link to Mask) shouldn't be used with any other group, since its mainly for new detectors.
Ideally the mask should be about the same size as the character itself, as it defines its boundaries/hitbox. Theoretically the mask can be whatever size you want (the collision detection is loop-based, moving the object itself), but you need to adjust the width of the Floor and Ceiling Detectors to match the mask, otherwise Jump-Thru Platforms and Crouching won't work as intended.
You can use a physics object without adding it to Group.2, but it won't look for any collisions (although the mask will still react to it). Group.2 also allows the physics objects to pause, by adding an additional Static movement to it. Click on the +/- button when selecting a movement type to add one. It seems not every physics type will pause though, would be nice if that option was built-in. :P Really depends on what you're trying to go for though.