Unfortunately that setting (the proxy timeout) is 100 seconds so if your origin server cannot return a HTTP response within that time, you will encounter a 524 error. It can only be customised for Enterprise customers.
Probably the best thing to do would be to find ways to optimise your git application so that it can do that operation in under 100 seconds, or explore ways to pre-warm that operation if that’s possible.
If you can’t do that, in terms of alternatives - you could try exposing your git service via a TCP tunnel instead (which should skip the HTTP CDN and the 524 timeout) or via Private Networking. Both would require you to be using the WARP application on the client side to connect to git.