If the source server is compromised then nothing can help you. All source links can be changed to something malicious and all verification methods can be different to match the ones of the bad file. If the source server is compromised there is no way to accurately verify the file's source (unless using verified PGP signatures which you've already vetted).
That's my point. Why go to the trouble of securing the transport layer if you're both NOT using PGP AND assuming with no proof that the server isn't compromised? I mean sure "security all the things" pays my ramen but at some point youve gotta wonder if you wouldn't be better off securing a trusted signature transmission method and comparing your insecure downloads to those provably correct signatures.
I'm not complaining, in the end clients assuming the server is uncompromised "because otherwise we'd be boned" and relying on transport security on top of that has secured me most of my work this past year... :)
