You only need permission if it's going to be released publically. For you're own use, or private distribution to family and friends, no permission is needed. As far as changing the terminus station, it's quite easy. All you need to do is search through the file for the .sta command for Tower Hill. This will be layed out in the following form:
.sta name;arrival time;departure time;(various other things that are irrelavent to this).
All you need to do is replace the departure time with = and this will tell BVE that this is a terminus. If you want to alter the platform though, so that the train goes into the bay, it's much more difficult, and would require the recoding of most of the route from where the train left the original route to the terminus. It can also be done with BRR, using random paths, but the results can be a bit hit and miss (if it works at all), and usually require some modifications to the original file to get BRR to pick up the alternative path, and of the final file to sort any issues with that. One important thing though, before you start modifying any BVE files, make sure you have a backup incase anything goes wrong.