Actually, the numbers signing from abrad are very small and tend to be from UK residents currently living on the continent.
I think this is missing the main issue with this petition. Those voting from abroad may be British expats or they may not be, we don't know, and you're right they're not a huge percentage.
The bigger issue is that there are a few million EU and non-EU foreign nationals who are not British citizens living in the UK who can vote in these petitions but are not eligible to vote in a referendum on eu membership.
They've all got UK postcodes as they live here so there's no way of knowing what proportion of the 3m votes are from people who were not actually eligible to vote in the referendum.
No one knows, but I'd guess a healthy proportion of these votes are from eu citizens residing in the UK with a vested interest in remaining.