I am not sure I completely understand your use case, but if you have 2 files with 100 import statements, what’s stopping you from having another one with 200? 
Joking aside, instead of using ES6 import and export statements, you might want to use the ES5.1 require() function and exports object k6 has, since they are a bit a bit easier to work with programmatically. You can loop through the exported elements of a script and do stuff with them, re-exporting them only if necessary, etc. Just keep in mind that it’s not the same as Node.JS’s require function.
You don’t need to be in --compatibility-mode=base to use requre(), you can use it in your ES6 scripts as well.