The ones without arrows or sheds are auxiliary beacons. I think they tried keeping the distance between the main beacons with arrows kinda constant and then if there were gaps or hard to see spots they’d slap down some aux beacons to assist with navigation.
Here’s a strip map of the route from Salt Lake City to Boise which shows the beacons with arrows, aux beacons and relief air strips https://drive.google.com/open?id=1-vIhYJ4Q_mQGG4yqi_yd7j-X5h-m1MbS&authuser=hobo.kurek%40gmail.com&usp=drive_fs
And another strip map from Boise up to Pasco covering the rest of the route:
The section in-between the north coast of the lake and Strevell:
There’s actually more aux beacons on the map than in the mod. The put a lot down in that stretch for some reason. Not many elsewhere. In the next release which covers route 32 from Portland to Pasco and then up to Spokane there’s a bunch of green and red flashing aux beacons either side of the Columbia River gorge to help you not fly into the sides of the gorge at night.
Misaligned flashing beacons are a constant pain. They are positioned slightly above the model because otherwise the model itself would block the light from certain angles and sometimes appear slightly off for some reason despite the co-ords being dead centre. It’s a weird one. Also missing beacons is another weird issue that happens in some places like at #10. Sometimes it shows and sometimes it doesn’t. It’s pretty baffling.