I make it a practice to open SSIS and SSDT as administrator to avoid annoying permission errors. This error seems to appear most frequently during the Data Flow process.
This does seem to be necessary since the introduction of the .ipsac file with the move to the project mode of development and deployment. It is annoying, however, and in my view reflects poorly on the project. However, I'm otherwise a big fan of the changes, so I'll make due. Hopefully this is on the list of things to be "corrected" for a future release.