There is no way I would use it on a transmission pan. If just a little bit of it got in the trans valve body it could clog it up easily, so it's a no go for me.
1. The filter would prevent that.
2. You're using way too much if that is a concern.
3. Any RTV that squeezes out just stays there, it doesn't drop into the pan.
4. Most modern transmissions use it instead of a solid gasket because it's superior in preventing leaks.