Generally I thought software in a github repo can be used free of charge, but your upstream website says free below 3GB.

The online service is not imapsync, it doesn't require any download. It's an online service, with no installation.

Is there a 3GB limitation when using the software in this repo?

There is no limitation here.
Neither at the upstream website by the way.
The upstream website says it's gratis under 3G but it is also gratis above 3G, there is no limit.
Have a try and see.
I restored the warning about 3G because the sales are cut by half without it.
It's a fake warning. To pay the bills and continue to work on imapsync.