Hi Jon,
I think the point you raised about geometry is very important; unfortunately I am afraid I have not a complete clear view of how to tackle the whole geometry in terms of use and meaning. Nevertheless, I would like to share some ideas I have about it.
I think I would still say that Euclidean geometry is completely harden.
The existence of other geometries didn't prove that the propositions of Euclidean geometry are false. At least not in the same way we say that the proposition 'the Earth is flat' is false. Rather we become aware of the background needed to use and therefore have meaningful mathematical propositions in Euclidean geometry. The background needed is the context of 'flat Riemannian space' (and all the contexts associated to it).
As you mention the meaning of point and line takes different meaning in different non-Euclidean spaces. Seeing the differences and similarities in use of those concepts in geometry is becoming aware of the backgrounds needed to develop useful propositions in geometry.
I also think that physicists should be concerned about philosophical discussions around the meaning of symbols they write down. I am sorry if my essay give you the wrong impression. The more physicist are aware of the meaning of the symbols they write the more they will be aware of the background and contexts where physics make sense. This clarity of background will allow us to identify useful empirical statements. This is not related with the true or falseness of the statements but rather with the appropriate context. As an example: The statement 'Romeo loves Juliet' is meaningless (it doesn't even make sense to ask if it is true or false) in a physics context, it belong to a literary context. We recognized the difference of background. However, there are more problematic statement that only philosophical discussion can clarify.
I will read your essay and comment on it. It looks interesting. Regarding the questions you pose. I think for example question 12) what is asking is to find a use in physics. That means until we can argue that your formal system with the extra axioms can be linked to the context of experiments and predictions there is not a priori physical meaning. Question 13) is asking for why does human regard some thing more intuitive that others. I don't have an answer. I believe that if what we want is an explanation then advancements in psychology, biology, sociology, neurobiology can provide answers. Nevertheless, at the level of description we are aware of this fact. This is a fact about human nature. If humans would have different intuitions our forms of live will be different.
Certainly, I will keep thinking about your post and if something becomes clearer for me I will let you know.
Kind Regards,
Yafet