Use the original 4:3 source for both. A finished 16:9 frame has already thrown away vertical information. Cropping that again to 9:16 forces you to work with a much smaller window than necessary.

You can share the same cut decisions, but the composition should be allowed to differ between delivery formats.

I duplicate the sequence after the story is mostly locked. One version becomes the widescreen master and the other becomes the vertical master. Then I adjust framing only where the aspect ratio demands it.

Titles and telemetry overlays often need separate placement too. A speed gauge that sits safely in the corner of 16:9 may cover the subject in vertical.

In VSDC I would keep both timelines or projects connected to the same original media, not to one another's exports. That preserves maximum source resolution and avoids an unnecessary compression generation.

For 360 footage the principle is even stronger: make a separate virtual-camera pass for each aspect ratio instead of cropping one flattened result.

That also explains why some of my vertical versions felt cramped. I was taking an already tight 16:9 composition and then cutting the sides again.

I will duplicate after the rough cut but reframe from the original source for each format.

That gives you efficiency without pretending the two formats are the same composition. Share structure, timing and source media; customize framing, graphics and safe areas.

The extra pass is usually much cheaper than trying to rescue a crop that started from the wrong master.