Consider for example the double parshah Vayakhel-Pekudei. The aliyos from the two individual parshiyos are combined as follows: 2, 3, 1, 2, 1, 2, 3. (Meaning: the first two aliyos are combined into one, then the next three are combined into the next aliyah, etc.)
Why not just combine each pair of aliyos from the separate parshiyos into one? (As far as I know, the only pair in which this is done consistently is Acharei Mos-Kedoshim.)
[Not really an answer, but some random stuff I found and some general impressions.]
The Aruch HaShulchan writes (OC 282:12):
המנהג הפשוט כששני סדרות מחוברות קורא הרביעי סוף פרשה ראשונה ותחלה שנייה כדי שהשבעה קרואים יהיו שוים בשתי הסדרות
When dividing up the aliyot of a double parsha, one should make the fourth aliya straddle the border so that each parasha gets half the aliyot. He quotes a discussion in the Levush what to do if one adds on to the seven aliyot: the Levush feels that the extras should be split between each parsha to keep the count even; the AH feels we only count the main seven in regards to an even split (he proves this from maftir).
I note also that the Temanim always make Chamishi of a combined parsha start at the beginning of the second parsha. You can see there chumash here. It seems to me looking through some of the Temani splits that they take advantage of the sparsity of aliyot to try and place them only at the 'better' stopping places, usually the parshiyot petuchot and setumot. I assume they feel that a Weekly Parsha (sedra) break is even stronger than a regular parsha (parshiya) break and that's why they always guarantee an aliya stop there.
I don't know if you're going to find a rule that covers all the different parshiyot. But there are some of the choices that make some sense. Consider the first three aliyot in Netzavim: the first two are quite short while the third is long. Presumably this is because the third has some negative content and we don't want to stop in the middle, but we need 7 stops, so we squeeze them at the beginning. When we have a double parsha, those will be the first to go. Similar considerations can explain the breakup of the beginning and end of Bechukotai, with the Tochecha causing a problem for aliyot. Finally, I think that the placement of combined-5 in Masei is there to avoid breaking up the list of the journeys, and a similar explanation can be given as to why combined-3 is at regular-6 not regular-5 of Mattot (assuming an a priori standard of 2-2-2-2-2-2-2).
Other than that I think it's just Minhag Avoteinu that developed somewhat out of concern for length and context. The aliya breaks as we have are a relatively recent phenomenon and I don't know that we can expect the process to have happened under the rigid oversight of an organizer. It's simply Tradition!
