I did a similar installation 10 years ago when I installed a storage lift. I added a dummy panel to the top of my garage door, which simplified the spring calculations. The extra panel is totally inside the garage on the sloping part of the track, is totally undetectable from the outside, but does look a little funny from the inside.
You chose a nice opener. I stuck with my 20 year old conventional Sears unit, so I have all that stuff hanging down. But, it works well. So far I've been too cheap to get your model opener.
I recently replaced my 2 old wood doors with steel doors and again did the installation work myself. As an engineer I did my own spring calculations.
The side with the lift freaked out the company supplying the doors & springs. I basically told them to ignore what's there and provide a spring per my calculations. It all worked out fine.
As to your comment on the "eyes" going out of alignment, I've never seen that happen. But, I have seen them fail with age. The lenses are such a wide angle that I had replacement units working when they were lying on the floor before I snapped them into the brackets.
If you have young kids around, the eyes make a lot of sense. But, without kids present, I have to agree they can be an annoyance.