I don't understand exactly what is the relationship between Mukdam UmeUchar Batorah and Klal Uprat/Prat Uklal. The order of the Torah is not chronology order, however there is the order of written, the same order Moshe got the Torah the same order he wrote it, this order implies the Derachim ShehaTorah Nilmedet Bahem even if spanned in two Inyanim. Why then the chronology order is important?
Good question. It seems from RASHI (DH Ein Mukdam, and DH d'Iy Lo Teima Hachi) that the concept of "Ein Mukdam..." refers not only to the historical events in the Torah not being written in the same chronological order as the order in which they occurred, but also to all the details of the Mitzvos that Hash-m told to Moshe Rabeinu.
That is, if it is true that the historical events were not written in the order in which they occurred, for whatever reason that may be (for example, perhaps they were written in a logical order, to facilitate learning them), then that same criteria would determine the order of the Mitzvos and details of the Mitzvos (that is, non-events). If so, we would not be able to apply the tools of Prat u'Klal, since other factors besides Drush determined the order of the words in the Torah, and Hash-m would have had to give us other methods of Drush that do not depend upon the order of the verses. Proof to this is that even by changing the *chronology* alone, we affect the Drush (as in our Sugya, where an extra Gezeirah Shavah is necessary because of Ein Mukdam u'Me'uchar ba'Torah), and yet the Torah goes ahead and changes the chronology.
The Gemara concludes that in a single Parsha, the importance of preserving the Drush through Klal u'Perat etc. wins out and therefore no other factors besides the Drush are involved in determining the order of the words/verses. Because of this, the chronology of events in a single Parsha will be preserved as well.