As I understand it, variable frame rates are used to lower the frame rate when nothing is changing on the screen, to help keep files small. So I assume that when a variable frame rate video is successfully converted to a constant frame rate, no one will notice – it’ll just fill in the “missing” frames with copies of adjacent frames – and the exported file will be the same. Based on what I’ve read on this site, Shotcut doesn’t like VFR files, so IF your source files are VFR you’ll want to convert them first and Shotcut will work better. (Screencapping CFR will result in the same or better exported quality; the screencap file sizes – not the final export – will probably be larger.)
According to Variable Frame-Rate video clips import with choppy video - #8 by EnzoD you can tell if you have a VFR file if the framerate shows up as 1000.
Your export settings question does seem to go beyond the scope of this “Bug” topic.
If you want expert advice, probably best to start a new topic with as much information as you can provide in terms of what you’re starting with (gameplay & facecam formats, fps, resolutions) and what you’re doing with it (youtube gameplay videos).
This guy, who is not an expert at all, will cheat and say that from what he’s overheard, it sounds like H.264, 2160p, 60fps, 85Mbps, GOP 30, B frames 2, preset=slower, profile=high might be the way you want to go. Start a new topic if you have questions.
(“overheard” at YouTube recommended upload encoding settings - YouTube Help , Suggestions for Smaller Filesize Without Losing Quality? - #5 by nwgat , and Output file size - what am I doing wrong? - #17 by Steve_Ledger )
(Just to reiterate: YouTube recommended upload encoding settings - YouTube Help is required reading if you want to talk about exporting to YouTube.)