The reason this is happening is because some VPN services will change your IP address and may even route your traffic through another country. Therefore, it looks a little suspicious to Firefox when you connect from Germany on Tuesday and then from the US on Wednesday and then from The Netherlands on Thursday.

Unfortunately, there's no way to disable that feature, so it's simply an unwanted side-effect of using a VPN service. You can probably limit the issues by manually specifying what country your VPN should be from (if possible), but just the fact that your IP address will likely be different each time you connect is likely going to trigger this problem.

I think I always knew what Firefox was doing as a response, but wasn't sure whether they had a way to manually circumvent the behaviour. I always use a VPN server local to my country; can that be whitelisted in Firefox somewhere?

To the best of my knowledge, no. It's likely happening because you aren't getting the same IP address each time you login to Firefox Sync, so the system thinks that you are logging in from a different location each time.