It's just a one time heal unless you hit the synergy, isn't it? Don't see it used enough to know for sure. Easy to test though, just need a friend. Glad I could speculate at you.
Transmutation is a somewhat weird set TBH.
I can get it to proc off of Sap Essense, which is clearly NOT a HoT but rather a somewhat delayed heal that does damage and then heals.
I haven't tested it with Energy Orb but I'm almost positive that it would proc it as well, I just don't have the skill points to unlock and morph to actually go about testing it.
Energy Orb is a HoT. It ticks once per second, if I remember correctly (I'm not able to check atm). The burst heal is from the synergy portion only. So, the answer is yes, it should work just fine with Transmutation. However, I haven't personally tested it, so if it's broken it should be reported. Energy Orb is definitely a HoT, and if Mutagen/Rapid Regen works for Transmutation then there is no logic that suggests it should not also work with Energy Orb.
The easiest way to test is just to have a friend open their character menu and see if their crit resistance value changes once you hit them with a tick from Energy Orb.