To be honest Aleksandar, I do not really understand any of your questions, since they are posed in terminology that seems very heavily laden with assumptions. I was not aware that Whitehead has 'two modes of perception'. Is that in P&R somewhere? What is an ultimate frontier of rational thought?
I do not think perception with presentational immediacy is in any way outside science. I think it is built in to all science, but that the more proximal you get in a dynamic chain the harder the ascertainment problems are. But then I am not quite sure what you are really asking. I forget what an 'eternal object' is for Whitehead. I actually think Leibniz is a much better place to start but Whitehead does try to address the problem of temporal divisibility  to make the dynamic unit an occasion rather than an immortal soul. Yet in the end I think he takes the wrong turning.

To be honest I find detailed analysis of Whitehead rather unproductive because it does not help that much in formulating a better system, which is what we are discussing.