Entities can be removed by adding commands in the script file. So if what blocks your bots is a door, barrier, shootable windows,etc then you should be able to do it yourself by extracting out the mapname.script file out of the mapname.pk3. Once modified the new version goes into your fritzbot\maps directory in your waypoints (pk3). This
fritzbot map scripting wiki topic shows the 2 ways to do it. As to removing brushes/clips like regular walls I am not sure since they are part of the "world".
as to the doors the bots understand how to operate func_doors, func_door_rotates so as long as your doors are that type they should be little problem. Doors that use buttons on the otherhand are often special script_movers and will likely need special handling.