So currently there is a config option called CombineStackedPrivs and it should be set to true by default. If it's true, then it a TC is raided then it should allow you to raid all TCs that are overlapping with that one (that share an owner). So in the situation I think you are describing it is supposed to allow you to raid a multi TC base at the cost of 1 raid point. If it's not working, seeing an image of the layout of the base in question might be helpful, there may be some tweaks I can make.
In general though, I chose to design this plugin such that 1 Raid Point = 1 Base for a number of reasons, and I don't plan on changing that fundamental piece of it. But it's definitely not intended for people to have to spend a bunch of points to raid multiple TCs in a single base, so if that's an issue I'll try to address it.