Yep, and because they value different things. Ask any IT manager in a corporate environment and they’ll tell you the absolute last thing they want is a “download store”. Or users installing a lot of apps, for that matter. The smart solution would be to build encryption in at the kernel level that accepts executables only from specified trusted sources e.g. “the company download store”, which would be highly restricted and business-only, of course.
Intel’s motivation will be as it always has been, to create demand for new processors, i.e. for more processing power. They’re very good at this, else we’d all still be running 386s.
Go over to apple.com and enter “iPad enterise” in the site’s search box. There’s a wealth of information there that covers all the concerns you’ve listed.