People bristle loudly over "home cooking" here. Best not bring that up. Suffice it to tell you that it is a LOT more rare than most fans believe, in that most umpires work all over, for multiple schools, teams, etc - and in almost every case, we REALLY don't care who wins. It's also a myth that we skew our decisions toward those that hire us --- frankly, there's more work than umpires in general. I don't know anyone that would favor a TD's team in particular just to stay on their good side to make it easier to find work.
As a fan, you're probably not aware that in ANY given game, there will be 10 to 20 (sometimes more) plays that are close enough that no matter what the call - the offended side will think the umpire blew it. You only notice, as a fan, the half that go against you. A fan on one side will insist that the umpire missed "at least 5 obvious calls" against us. A fan on the other side will say exactly the same thing. It's the nature of the game - and neither fan even notices the once that were close but went in their favor. And trust me ... you REALLY can't see what you need to see from the stands. If you could, we'd umpire from there.
That out of the way...
I will agree that it's uncomfortable (at best) to have a TD as a coach - it should really be avoided. Let someone else TD, especially when you're on the field.
At the very least, in your particular situation, the PU to F2 conversation should have been relayed to TD - at least after the game. He needs to know what he's got working for him. That was completely inappropriate.
During the game, however - when the overrule happened, your coach should have used the magic word. At the very least it would bring the inappropriateness of the overrule to TD's attention (yeah, he was there on the field, but given that he's chosen to take on both rules, he has to at least be aware that what happened was not appropriate... a TD who runs an unfair tourney is not going to get any returners, so even though he's opposing coach, he HAS to take the other coach seriously. Perhaps there was a UIC somewhere on premesis that could have done something to correct this erroneous decision.)