Is there a machine out there that won't throttle, given a sufficiently heavy load? Similarly, there isn't a machine that won't go into thermal shutdown if it gets sufficiently hot. That's the point of thermal protection - to keep people from pushing the thing beyond the redline.
The only question here is, all other things being equal, will the 14" throttle when the 16" does not? The answer to that question requires hands-on testing, not guesswork.
Speculate all you want about thermal design and thermal load. Bigger is not necessarily better. The 16" is larger to accommodate a larger display, which makes thermal demands of its own on the batteries and power supply. That larger piece of aluminum allows for more passive cooling. That may mean the fans in the 14" kick in sooner/run more frequently than they do in the 16". Or, yes, Apple can choose to throttle the 14" so that the fans kick in no more often than they do in the 16". We Just Don't Know.
So, instead of making a decision today based on people's optimism/pessimism about Apple's latest thermal designs, wait until there's some hard data to work with.