I just want to preface this comment with I appreciate that Godot has had different development priorities, and is a great solution to the types of projects that OKAM have had use cases for. A priority for us is how 2d performance can scale to highly dynamic platform games and simulation projects in the vein of prison architect etc
I agree that this many allocation per frame is not a huge concern, but this is also a very simple scene with just a few scripts running. If allocations scale with scene complexity then this number could get into problematic side effects. You are at the mercy of the platform runtime as to what it feels like doing on each call, as you say malloc is (relatively) cheap, but can also cause hard to track frame spikes later in the project cycle.
A greater concern to me is cache consistency when various systems are walking the heap to do their work. This in our exp is the number one performance killer that is very hard to solve with profiling alone as there can just be an overall feeling of slowness that does not really spike anywhere.
To move forward from this (as you also say) we would want to identify a test scene where this is actually an issue. From here my plan would probably be to try to identify allocations that are really used frame by frame and move these to some sort of stack allocator that can be refreshed each frame. I would also want to try to identify areas, such as command lists, and make sure these are being walked in linear memory, this may take some more heavy handed re-factoring (no idea yet)
In terms of identifying what systems are making high use of allocs, I would probably start with adding some functionality to your current alloc wrapper to give some watermarks for various systems, but to be honest I usually start by just putting a break in malloc and looking at what is calling each frame, then start to look at a system as a whole.
QA does not seem like a good fit for discussions such as this, if we feel we can contribute, is it better to open a forum thread or open a github issue for this kind of thing?