When you disable Safe Browsing, both should be marked as ‘dangerous’.
Sometimes other files are an exception to the ‘always mark them as dangerous, because we can’t verify them’ since they have a signature and all that.
Eventually this is not going to be a problem, because Brave released a flag to avoid this danger message in Nightly yesterday:
Override download danger level
Disables download warnings for files which are considered dangerous when Safe Browsing is disabled. Use at your own risks. Not recommended. – Mac, Windows, Linux
It’s strange that it marks both for you. I tried again and the second one is not marked for me, nor most of the jar files I download. And those were all new files that I had never downloaded before, new filenames, new content, so I’m not sure why it’s flaky like that for me.
It’s nice that a flag to block this message has been added though personally I actually like the message, I just didn’t like the possible implications of having it show only for some files, because to me it seemed like it was using some kind of reputation service.