MacBook Pro Retina Late 2013 slow down with 65W charger?
I would suggest that your analysis sounds completely reasonable.  

I have a 2013 MBP without a battery and it runs at 1.2GHz instead of 2.4GHz unless I override the BDPROCHOT setting that is set in the case of missing battery.  CPU throttling to half speed is well known if battery is dead or missing.  See here,here and here as random examples. 

Lets assume your PC has a I7-4850HQ this has a maximum TDP of 47W.  Add to this the demands of rest of the PC, your extra peripherals and you are easily using more than 65W so you drained the battery to zero (as you said) and this CPU limiting kicked in.  

I'd suggest to prove it you download Intel Power Gadget and it will tell you the amount of power your CPU is using under whatever workload to which you can add your other peripherals.  Here you can see my CPU is using ~40W on a similar 2015 mbp to yours with the jump in power usage just being due to rapidly scrolling up and down in Firefox for the sake of this picture.



You can use various software cap the amount of power your CPU will use but that is another question.