Gas prices are calculated by looking at config params 20 (for masterchain) and 21 (for basechain). As long as they are the same, the calculated gas fees will be the same.

I checked it and currently on the basechain they're equal, but on the masterchain, they're not.

Also storage fees are dependent on the runtime state of each account, so they'll surely be different, although usually it's a very small fee.

There is also a forward fee which might differ depending on the blockchain configuration.