I use GIMP and they use scripting to get a LOT of their features implemented, esp. in applying filters or effects. These scripts are integrated into the main program, and i wonder if you plan to do the same. I would hate having to run it from a separate console, but with MPT's tight code, there may be no choice, at least at the outset.
I'm not sure what your question is referring to, but i would think we should be able to run any script at any time, even combining where possible.
Also consider time needed. I for one would much rather have capabilties right away and establish better GUI later, and if it's gonna take a LOT longer to integrate scripting in order to get everything you want now, let's go ahead and enter the new construction with all the 2x4s showing rather than wait for a perfect mansion with all the amenities you've been planning on.