I had none of these issues and i don't know what you are talking about.
If you install programs through your package manager they come with a start-menu entry just as easily findable as in Windows. If you don't install programs with an installer in Windows you get the same problem.
Also mounting HDDs made its content accessible to all my programs so far, without any issue. I think you must have chosen extremely obscure distros or fucked things up by yourself during install processes.
I always found that deeply problematic. Here is some obscure path to follow to set some obscure value where half of the naming does not indicate what exactly you are doing there. Also if you don't set the data-type exactly it wont work. For a fucking 0 or 1 off/on value flag.