I've created a custom profile with 350x260 resolution 30fps. Now I import a 2288x1080 video, zoom at 200% and pan til the desired part fits the rectangle. Then I render the video with Rescale disable and the resulting video is actually 350x260 and Buffer dimensions 352x272 according to VLC.

What's the issue?
You have your output 350x260!

This is a question easily answered with a simple search, it is not necessary to create a new topic.

I don't use VLC but this pixel difference is relative to the codec's operation it is probably trying to turn dividable by 16 to be able to use a block size of 16x16.
Those extra pixels are blank