Testing Method:

Both download a fresh version of the mod from the same source
Zock hosts 1v1 game of FAF BETA
We play a bit
Single desync observed ingame at beat 101. It does not repeat. Apparently this is normal.

local replay is the one at programdata/FAForever/replays

.fafreplay is set to launch using the client .exe

Results:

Zock testing his own local replay - No Desync at all
Zock testing server replay launching from client - Desyncs constantly
Zock testing server replay launching from file downloaded via browser - Desyncs constantly

IceDreamer testing his own local replay - No Desync at all
IceDreamer server replay launching from client - No Desync at all
IceDreamer server replay launching from file downloaded via browser - No Desync at all
IceDreamer testing Zock's local replay transferred via Dropbox - Constant desync
IceDreamer testing the exact file that desyncs for Zock, transferred via Dropbox - No Desync at all

What. The actual. Hell.