Hello and good to see you back! I remember you hanging around before and I believe also announcing you were moving and wouldn't be able to pursue the build when initially planned. I'd highly recommend keeping all of your questions in one place going forward. It becomes much harder to follow the flow if there are multiple threads for the same build. The reason your Fastlane was not so familiar is that they are probably installed on .x% of pools. And autocovers are probably just a few percent, but way more. I will be interested to see the Fastlane follow-up you noted above. I'd be very surprised if there isn't a good alternative for a vinyl IG pool with an autocover. All of the plumbing and intake should be either on the bottom or sides and not have to be at the water surface like the one you show. I think you will build a very good following for this thread as it builds momentum.
Regarding equipment being below the level of the pool. Sure, no problem. Not the most popular but quite common. I think instead of the valves being discussed above, which yes you would need to consider specifically for your setup, you would need to ensure proper installation of check valves. They would be the devices that will keep the water in the lines from draining out shoud there be an opening in your system. So if for example, your pump cover had an o-ring that wasn't sealing properly, when the water is shutoff, a check valve immediately after the pump would keep the water that normally flows towards the pool from draining back down and out through the system opening. Or if you are cleaning your filter, no need too change valves, the check valve should do the trick. A valve would just be a back up or to allow for some other operation as well.
You will definitely want a Wi-Fi switch on your autocover so you will be alerted when it is opened and also be able to check the status of the cover remotely. And perhaps there is something you can set for alerts if the cover is open more than x number of hours, etc.
Looking forward to seeing your progress and questions! The common term used for pools like yours is Owner Builder (OB) when you will be the general contractor. Knowing that you may sub some off the jobs out to yourself if you provide the best return on your investment. Searching by that term will also guide you to many threads that may be insightful.
And lastly, a few good overview before pictures would be great to help us see your vision more clearly!