yeah, showing up with a stack of papers and not knowing whether they want the funds "seasoned" for a certain period of time means doing a border run is preferable.
Has Taipei already transitioned? I think they will soon, but it hasn't happened yet. I doubt there will be more questions when applying via e-visa...it will be a case of whatever you end up submitting and whether they ask for more documentation.
It seems that all visas issued in sticker form still state "employment prohibited", meanwhile some of the e-visas now say things like what's indicated on your visa.