All spaceships have transponders that identify them, are vital for fleet/spaceport navigation, and are illegal/difficult to modify or remove; which the rebels did not routinely do.

Okay, first of all, this is absolutely bonkers for military spacecraft. For a fighter -- a spacecraft designed for combat -- such a system should be easy to disable with just a switch in the cockpit. To have a transponder that automatically identifies you even to enemies is a huge disadvantage for no reason. Absolutely ruins any pretense of stealth/surprise, could easily be used to augment enemy target tracking...

I don't quite buy it being difficult to remove, either.

But especially being illegal to remove really shouldn't be much of an issue for an active rebellion. Removing a spaceship transponder is the very least of the illegal things they've been doing.

It makes sense a vehicle make and model would be enough for one of the galaxies best bounty hunters to go off of.

No it doesn't, not at all! There were dozens of X-Wings involved in the assault on the Death Star. And there were probably hundreds of thousands, if not millions, of X-Wings all over the galaxy. To track one particular one -- and its particular pilot -- down, you're going to need a lot more than just the spaceship model.

Also take into consideration, the entire rebellion at this point is taking pains to remain hidden and difficult to find, and they're not going to take kindly to bounty hunters working on Imperial contracts.

But supposing that Boba Fett is just somehow that magically good at finding people ... in that case, the Empire wasted a lot of time and resources trying to track down rebel bases when they could have just asked Boba Fett to find them. If he can track down a single particular rebel pilot based on extremely sparse information, finding an entire rebel base should be no problem at all.