Varint encoding is something I've peeked at in various contexts. My personal bias is towards the prefix-style, as it feels faster to decode and the segregation of the meta-data from the payload data is nice.
But, the thing that tends to tip the scales is the fact that in almost all real world cases, small numbers dominate - as the github thread you linked relates in a comment.
The LEB128 fast-path is a single conditional with no data-dependencies:
if ! (x & 0x80) { x }
Modern CPUs will characterize that branch really well and you'll pay almost zero cost for the fastpath which also happens to be the dominant path.
The recent CREL format for ELF also uses the more established LEB128: https://news.ycombinator.com/item?id=41222021
At this point I don't feel like I have a clear opinion about whether PrefixVarint is worth it, compared with LEB128.