1. Is there any sort of "trick" to getting scripts to run while playing a scenario with a modded version of the game?
2. Are scripts only supposed to run with "custom game" playfield setups?
It was my understanding from the game documentation that scripts which are placed in the proper directory (e.g., on my rig it is):
H:\Users\Users\Documents\My Games\Capitalism Lab Post-Release Beta\SCRIPT
will run, i.e., one does not have to choose scripts to run from the in-game "Scripts" tab on the game setup pane (which only seems to appear when in the custom game game setup pane).
My mod "DicheBach.MOD" (which is really just my avatar swapped out for one of the default person.pngs) works fine. No issues at all.
My scenario "Writing the Big History" (which is still a pretty basic template for a more elaborate mod) also works fine. No issues at all.
My scripts: as far as I can tell they are not working at all: no sign of any autosaving, the first prospective executive staff member I try to hire wants $9.5 million salary per year . . . no idea on the tech costs yet haven't played it far enough to get to major R&D and actually wouldn't even know how/where to look to get a sense for my tech costs.

Maybe I've missed one important thing in the documentation (which might explain the whole thing): in order for scripts to be viable with a scenario, they have to be specified in the scenario files?
Unless there are already is such functionality, I'd suggest a couple things:
1. Give the user a way to see what mods/scripts/scenario files are loaded. If there is a ~ game console command that might be the most obvious way to do it. Or, a sub-screen of the options screen would be another
2. Change the game-startup selection pane so that scripts can be selected for a particular match (the way they can for "Custom Games"). I realize this could be complicated: there is a certain element of "social competitiveness" surrounding the scenarios and that is a good community-driving dynamic. As such, Scenario designers might not want particular scripts to be useable with their scenario (especially the cheaty ones!). So this suggestion might depend on (and all this assumes that there is not already functionality that links and limits use of scenarios and scripts as I asked up above there):
argument in scenario that either:
A. turns scripts off completely (makes it impossible to run any scripts with the scenario)
B. turns all scripts on universally (makes no restrictions on using scripts with the scenario)
C. turns scripts on specifically (scripts are default restricted, but allowed if their path is listed in one of the scenario files)