Background - I'm using a Galaxy S4 Google Play Edition, which is as close as you're going to get to a Nexus device with expandable storage. I've also done a lot of troubleshooting for a few developers (though haven't written any apps myself) regarding the KitKat MicroSD restrictions prior to them going mainstream. It sort of helps to have the first official device on KitKat with MicroSD.
1.with the stock file explorer (not 3rd parties) copy from internal memory and paste to sd micro card .apk files (not installed)
If you purchase a phone with a built-in file manager, this file manager can be granted system level permissions if the OEM wants it. In this case, you can fully manage data on the internal storage and the MicroSD.
As you noted, third party file managers (E Strongs, Astro, etc.) will have very limited control over the MicroSD. For most devices, you can read the entire SD card, copy data FROM sd TO internal, but not the other way around, and cannot create/edit/delete content except with the /android/data/app (com.estrongs.etc) folders.
Some Samsung 4.4 devices have a work around, but there's no guarantee that this will remain through the next OTA.
with the computer help via usb, copy from internal memory and paste to computer,copy from computer and paste to sd card .apk files (not installed)
USB support is unchanged. You can still manage data via USB hookup as before.
(Nexus devices also don't have SD cards, so not really relevant anyway).
There are now 4 Google Play Edition devices running stock Android with KitKat and MicroSD. It's not branded a Nexus, but the concept is the same. None of them come with a stock file manager, aside from Google's Storage Access Framework (SAF).
It's been a while since I've used a phone with an SD card, but I believe that both a physical SD card and the emulated storage internal to the phone (which may actually be referenced as an SD card) would both be treated as Internal Storage. They would have the same permissions and restrictions applied.
Unfortunately, they're not. Actual internal storage (often mounted as .sdcard and /emulated/x) uses the ext4 file system, which allows for per-folder permissions. The external SD card (now mounted as /ExtSdCard) is formated as FAT32 which is all or nothing in terms of read/write. So it's all read and no write for third party apps. The /android/data writing is actually done to the internal card and moved over by the system to circumvent this restriction.
With that in mind, though, any file explorer *should* be able to copy files between the two unless the files are a part of any application's protected storage area.
Due to the different file systems and associated permissions granted with KitKat, you can copy date FROM sd TO internal, but not vice versa.
The same should hold true when moving files around from your computer.
Once mounted via USB, it's your desktop's permissions as opposed to the phone's that take over. You get full r/w permission from your dekstop via USB.
