Yep, old alignment of GPIO and IR was bad. But new is awful. You still have problem with modules which interfere with finger. And IR usability is broken because you can’t point on device in front of you and use arrow keys naturally.
This how it should be:
One more thing to suggest, but not shure. USB-C can be moved from right side to bottom-right corner. Right side is fully closed by hand and there is no way to use flipper comfortable while charging. If USB-C will be on bottom - we will get two features:
If you would have any kind of antenna module or bigger module, i would prefer to have it on top side, the same with connecting just pins, bottom side would be really bad.
Charger is minor thing, flipper can be hold even with side connection, but you would have to swap it for card reader hole, where bottom side seems better to me (limited interaction with card that way). Anyway this is something i would not mind both ways.
Hmm, goodpoint about antenna module. But huge antenna pushing module on top of device is more fragile. What about this align of huge antennas?
You have a point, but your design suggests all add-on modules would not have their own transmissions.
Like an IR thermometer, it would have little sense to snap it onto the back panel facing your body and being “unable to naturally aim”.
Since no one knows which 3rd party addons would even surface - which options has less downsides is a guesswork anyway.
Since there are two GPIO arrays anyway i wonder if they could be separated, one GPIO port facing forward, and another port moved to the rear panel like you suggested.
But this half-hearted (or flexibile? depends on one’s perspective) approach would probably have downsides too.
I wonder if someone woulkd do a simple mirror appliance to reflect the IR line of sight to the direct aim line like you want. Should not be hard to do 
