Hi there,
glad you enjoy our server and its configuration!!
What you are talking about (time bonus and maps customization) is mapscript (basically .script file already provided in each map pk3 which we modify). Then we upload these custom mapscripts in a dedicated folder on the server and a cvar on server config points to it. So it is loaded along with the map when server starts it, instead of the original one present in the map pk3.
By the way, most of these custom mapscripts were/are done by a friend of TM, and I encourage you to contact him to ask if he agrees to share them. He is @uips. If he does agree, i can dump the whole folder and share it with you.