koko,
I have the skimmer transducer epoxied in my hull. It works great and I have read the depth while running at 55mph plus. The puck is a little easier to mount inside the transome but you don't have to have it. Yes, you will lose just a smidge of sensitivity but I doubt you will really be able to tell a difference with the HDS. You just have to make sure there are no air bubbles in the epoxy after you install it. Just keep moving it around a little bit while glueing it down and you should be alright. This also has an advantage. You don't have to worry about tearing off your transducer on some trash floating around in the lake. As far as temp goes, you can do your reading off the front unit as you suggested. You said that it will only work when your trolling motor is down and that is fine. Do you really need to know the temp every second of the day? I just glance at my temp every now and then after the trolling motor has been down for a little bit to see if there are any big differences.
The only way to have a good fishing spot is to make it yourself!