The file system permissions issue is just a fundamental difference in how operating systems work. Android is based on the Linux kernel and Linux itself is based on Unix. Your phone's filesystem is ext4, a common and Open Source file system used in Unix-based systems. In contrast, most microSD cards are formatted using FAT32, Microsoft's old default, proprietary file system (currently NTFS). The problem boils down to FAT32 doesn't fully support Unix style file permissions, nor does it support metadata the same way.
So while your phone's internal storage media is formatted as ext4, where the operating system and the file system work in unison with the file and folder permissions, most microSD cards on the other hand, using FAT32, are not so complementary. Files and folders residing on FAT32 media require more resources for the host operating system to keep track of. And when you dismount and remove your microSD card and use it somewhere else, the files themselves will be fine it's just that their individual permissions and metadata don't necessarily go with them.
For more on Linux file/folder permissions:
http://ryanstutorials.net/linuxtutorial/permissions.php
Years ago when USB was becoming really popular the USB standards board (USB-IF) decided to adopt FAT32 as the default file system for USB gadgets. There's good and bad with that.
The Good: instead of some devices being able to work only with certain platforms, by establishing a default file system USB devices with storage media would be platform agnostic. Items like USB stick drives can be used with just about any computer as any modern operating system now includes integral, basic FAT support.
The Bad: Microsoft now has a licensed cancer that permeates into a lot of USB devices. Logic would dictate that adopting an unencumbered, license-free file system would have been a much better choice but sadly that just wasn't to be, money and corporate politics determined our fate. (USB-IF is a registered non-profit but it's definitely not a social services non-profit, it was created by a handful of corporations.)
https://en.wikipedia.org/wiki/USB_Implementers_Forum
One example that highlights Microsoft's proprietary FAT as a problem is the MS vs. TomTom lawsuit. Microsoft's legal department opted to go after a company that had an established USB implementation in their product and when the dust settled MS profited yet again and (cough, cough) justice served. MS can rely on even its outdated, minimally functional FAT as a money-maker.
http://arstechnica.com/gadgets/2009/03/microsoft-and-tomtom-settle-patent-dispute/
And of course there's plenty of backstory to this lawsuit. Corporate politics suck balls:
http://www.zdnet.com/article/microsoft-litigate-on-fat-and-youll-be-the-next-unisys/
http://www.geek.com/chips/clever-linux-folk-find-way-around-microsoft-fat-file-system-patent-824951/
