Father explicitly states they haven't been above ground in a long time due to radiation, but fine, I'll take your 3 examples as proof the Institute sometimes ventures above ground. Doesn't prove they have contact with the above world though given how 2 out of those 3 interactions are only with your character.
Alright, I missed that one. Still a really stupid reason to shut down an amazing program with the only excuse being "Father wills it" but whatever. I'm still calling it a complete cop-out just so they could have the excuse of giving Shaun cancer so you could take over the Institute and/or have an "emotional" moment with your son.
Oh yes, because 10 years of research with only ONE positive result means the whole thing was a success yeah? No, not at all. And second of all, Virgil doesn't count. He turned himself into a mutant along with making some bullshit miracle cure for himself. He made the FEV he injected himself with special, in other words, without jurisdiction or authority from other Institute scientists. What he used on himself was something completely different than what was used on the other mutants. He even says himself that the cure he made can only be used on himself because he injected himself with a unique strain of FEV that would let him retain his intelligence. For that matter, if you wait too long to bring him the cure, he eventually goes hostile, indicating the fact that he goes feral like the other Super Mutants if you take too long to cure him.
It does have to do with tracking, go back and play through the H2-22 quest line. Here, I'll even pull up the mission names for you:
http://fallout.wikia.com/wiki/Boston_After_Dark http://fallout.wikia.com/wiki/Memory_Interrupted Both Doctor Amari and Old Man Stockton talk about it. The memory wipe is something completely different than changing their appearance. Those 2 don't mutually go together. Not all synths have their memories wiped, as proven by Glory in the Railroad HQ.
For that matter, where is it mentioned that synths can magically disable the chip that would be used to track them? I certainly don't recall that being mentioned anywhere at all. Considering it's lodged in their head, it's almost impossible that they would be able to do it on their own without some sort of outside help.
Finally, yes the Courser chip allows the Courser to teleport around, but the Institute still has full control over it. For example, if you start to piss the Institute off after working with them, Father himself will teleport you into this little prison-like area and berate you. He teleports you using the same signal that you use to get in the Institute, meaning that yes, the Institute has complete control over their teleportation technology.