Unfortunately it’s hard to get the best of both (well, this is usually the case). The reason the common source has to be based on C++ is that that’s what the Arduino code is based on. This way it will maximally share the code base, with the goal of making the two versions fully compatible. You will see that the code isn’t that difficult to understand and expand. However, C++ is not a scripting language after all, so it’s definitely not as flexible as Python. I am not sure if there is a easy way to enable run-time plug ins. Most likely you will have to add code and recompile the program. But it’s not that hard.
As Linux is a multitask system, you can certainly run other programs in parallel.
Regarding the heat dissipation and reliability, that’s a commonly asked question and is certainly a concern. I honestly havne’t tested it thourougly myself. The Arudino version requiers less power and you are right that it boots quickly. So that’s an advantage. Overall as I’ve said elsewhere on the forum, the Arduino version is focused on providing an out-of-box working solution, while the Pi version is for users who have experience with RPi and prefer its flexiblity and extendability.