The problem is that in DSM 7, the installer has very little privileges. Synology heavily restricts what is allowed. That is why when something does not work, manual intervention is usually required.
@ChuckPa handles the packaging for all the Linux distributions (and a ton more stuff too). He worked with Synology and convinced them to lessen some restrictions. If it were possible to further refine things, he would have found a way.
The good news is the incremental DSM 7 updates to 7.1 and 7.2 did not present any major problems, so we seem to be good to go for awhile (until DSM 8 shows up some day 
).
FYI, The Synology FAQ - Questions, Answers, and a few How-To’s has a lot of useful info regarding running Plex on Synology. The procedure above is just a tweak of FAQ 26 Migrating from DSM 6 to DSM 7. It basically backs out the broken bits then re-runs the migration.
