Questions about Link2SD and SD card partitioning
yes, stock rom does not support other file systems but EXT2 for the second partition. So create an EXT2 partition.

the location of the apps, once linked with link2sd will be from the root of the sytem:
\ (which is root)
sd-ext
and there you will find some directories or app-files, depending on your link2sd settings.

About the question for mounting / rebooting: I cannot answer that because I do not know.

about the size of thee partition: when you connect your phone to your computer, and have minitool partition wizard installed, you should be able to create the partitions like you want it and with the size you want. 

But to be honest: 6gb for apps is an awfully lot... I think the tutorial just points out that you probably never will exceed the 2 gb that is mentioned and you can use the other 6gb for normal storage (which also can be read by windows when you connect your phone to your computer)

I hope I answered your questions...