Here's my registry entry. I've never seen that extra entry appearing though.
[HKEY_LOCAL_MACHINE\SOFTWARE\Cakewalk Music Software\Tools Menu\7iZotope RX 4]
"ExePath"="D:\\Apps\\iZotope\\RX 4\\win64\\iZotope RX 4.exe"
"MenuText"="iZotope RX 4"
"StatusBarText"="Run iZotope RX 4"
"Type"="WaveEditor"
"RegionFlag"=dword:00000000
Important to note, the reg text dump shows paths with double slashes, but inside regedit they are just single slashes.
I never run anything as Admin (though my account does have full escalation rights).
One thing that is kind of strange about Platinum (that I don't remember seeing in X3e) is I can't open a wave editor on a Groove looped audio clip. Only "plain" audio. It may have always been like that though, I just can't remember.
As for what/who/when that extra registry entry is coming from the best tool for debugging that is the Microsoft SysInternals tool Procmon. It can log every single file and registry access any software makes. I often use it to work out why software has gone wrong and to figure out what software is looking for.
https://technet.microsoft.com/en-us/sysinternals/bb896645 Bad news though, it's very technical and not exactly a end-user tool.
As for the multiple apps sharing the driver problem it really depends on the driver developer. Some are better at sharing than others. My Saffire will share (with or without the Sonar checkbox) as long as every ASIO app agrees on the sample settings (48khz). Software that uses MME mode will share anything, it's only the ASIO driver that has control issues. Hence my reason for letting Sonar have the ASIO and my wave editors use the MME device. This works because (for example) other apps can still play bells/Skype notifications/YouTube/Browser sounds/etc) even when Sonar is open. The MME driver is much more flexible than ASIO drivers.
Running Sonar as Admin will vastly effect how it launches other apps. And those other apps may not be very friendly when running under settings they weren't installed with. Temporary file paths are very different. Access rights are different. The registry is different. Network file shares mounted as the user may not be available. It's just a bad idea to run software as Admin without a very good reason a full understanding of what that may involve.
If I were having problems I'd use Procmon to record everything and look at what files Sonar and the wave editor are accessing and then try and figure out why/change that so it's correct. I'd also consider deleting all the tool menu entries from the registry except one (back them up with regedit). Might want to reboot once too (though usually that's a fools errand).
One handy tip, Sonar sorts the tool menu (technically the menu is now called Utilities but the second half of the Utilities menu (after the seperator) is the "Tools" menu) using the names of the registry entries (which isn't the same as what is shown to the user) so you can stick a number in front of the name in order to control the order. As you can see above my RX4 entry is named "7iZotope RX 4" since I want it to show up 8th on the tools menu. (I have tools numbered 0-7).