Well, we certainly don't based on your post, which is mixing up three separate stories - all of which surfaced at different times and involved different sites.
The story of an avocado-shaped UFO that crashed in the vicinity of the Trinity site in 1945 didn't surface until 2021, in the book
Trinity: The Best Kept Secret by Vallee and Leopizzi:
https://www.amazon.com/Trinity-Secret-Jacques-F-Vallée/dp/B09KDWDPZ1
The Project MOGUL documents were declassified and made public in the 1990s. No MOGUL flights were conducted over Alaska because they could have been conducted anywhere. The MOGUL instrument (essentially a recording barometer) was designed to record pressure waves propagating
worldwide in the stratosphere - waves which had only recently been discovered to both accompany huge explosive events (including the US A-bombs) and travel all around the globe at high altitude. The single USAAF facility handling high-altitude balloon research was in New Mexico, so that's where the MOGUL balloon arrays were launched.
There was nothing to hide, because Newton and Gebauer made the whole story up. They were the sole sources for the story, admitted it was a fraud, and were convicted of fraud in a court of law in 1953.