I suggest you take a deep breath and review everything you did, before removing any fluid at this point. If you refilled with the same amount of new fluid at the same ambient temp as the old fluid, and didn't spill any, then there is no possible way the fluid level is higher now than it was previously. I've done this many times on various vehicles, and there is never a change in fluid level when done as described above. Perhaps you're not shifting through the gears, or the running fluid temp is different, but in any event, the (properly) measured exchange will never result in a fluid level difference. .

AFA the rust on the pan, it's most likely just surface rust at this point, so just sand it off and repaint with a top quality high temp rust inhibitor paint.

 

Remove the excess fluid(or not), drive the vehicle at least 25 miles and 45 minutes of running then recheck. Then Add or subtract to be at or close to the full mark. Unlike engine oil in the sump if you run over the limit needed you are not going to interferer with a rotating assembly (crankshaft) that can cause cavitation and other negative effects. The dip stick low side is the most important value to make sure that you at least have the fluid in the sump (pan) so that the oil pick up will never be without oil.

Many transmission pans for years (decades) never even had paint on them. I agree that it looks more like just some normal rust forming from the normal use of the vehicle. Looking at the pictures you are not one to keep the underside and engine compartment cleaned very often! You can spray some paint on the pan after cleaning up the surface rust most any automotive engine or home BBQ will do.