With regard to Trump, there was a lot of media reporting around him being sloppy with classified material, etc -- and it's entirely possible that career intelligence professionals, aka the "deep state", took this into account when putting together briefings for him. But aside from that particular presidency, generally speaking, the commander in chief is almost never briefed on details of sources and methods for the most sensitive SAPs, simply because of the general principle of "need to know", i.e., if you want to keep something secret you should tell as few people about it as possible. With that said, the highest levels of the EB are certainly briefed on the key insights delivered by said SAPs.

As far as Los Alamos, aliens, etc -- super interesting topic. The recent UFO footage released by the Navy sure does make you wonder. Who knows....