No, never did. Believe the proper place for mdeploy files, etc. is in moodledata directory. Have a server that uses some 'big' plugins ... at least the zips are larger than most ... and have noticed/experienced they didn't update well via GUI mdeploy. Seem to get stuck after the current code plugin directory is removed ... which means half way. Can see the new code zip present but no 'activity' towards using it - at least I've not found a way to see that activity.
Anyhoo, Have resorted back to manual updates for those via hide, wget, php script in admin/cli.
Would assume that once the DB is updated with version information etc. that all those directories not really needed. There is currently no method via the GUI to use those previous versions in a 'rollback' as far as I know/can see.
However, my experience may not be yours! So on the side of caution, one could archive, save out to another handy location, in case I was wrong!
My 2 cents ...
'spirit of sharing', Ken