This may seem a dumb question but its not cause Im in a situation where it would be helpful. But basically, instead of rooting an Android phone by some app native to Android, does this seem possible:

Could you enable debugging, hook an Android phone to a Linux PC, find the system and data directories and somehow by a terminal take complete ownership of them? Isnt that what a "chown" does or a "chmod"? Im battling an intrusive update I installed by accident from Motorola and Verizon. They effectively took my old ROM and system which was rooted and unrooted it and like locked everything down. I cant install Clockwork Mod recovries, Safestrap bootstrapper nor even use any of the one-click-installs out there as I get permission errors. 3rd party apks that are trusted such as asc Superuser and Safestrap are getting forced closed. And whats worse, fun and useful apps such as my MXPlayer when playing a video are now popping up ads within them when they used to never. I even got a Motorola privacy statement saying they could now use my browsing history for their research, etc. This is bad. If I cant fix this back to rooted, Im tossing the phone through a Verizon store plate glass window. Any opinions?

Well, I'm glad to say I fixed all that somehow. As for what I did from Linux, I did go into KDE, downloaded Krusader and ran it as root mode. Then I just mount the phone's internal storage and set the permissions to r w x all the way through. Then I disconnected the phone, performed a factory wipe and cache wipe, and when it booted, tried a couple android apps I'd had in storage from a while ago and started executing the first one that would root me successfully. And sure enough, this all worked. I've got Superuser back and all that. What the exact thing that fixed this whole mess, the world just may never know...

Phones are still viewed fundamentally as appliances, not computers in their own right, so the emphasis is on reliability and consistency more than customization and control. Also, phone companies tend to view the phone OS as a tool to control the user, more than a tool for the user to control the phone. Since the phone is the revenue pipe to whatever phone company you are bound to, this battle will undoubtedly continue on.