Why the trup alternation in Yisachar, Binyamin, and Naftali?

Congratulations to Mi Yodeya are in order for getting their proposal accepted. They are now part of StackExchange. Here is a question on the trup of Bamidbar I answered over there this morning. If we examine the trup in the beginning of parashat Bemidbar, we find some slight alternations on the first word of a more or less repeating clause, though the rest of the trup is the same:

אֲחִירַ֖ע בֶּן־עֵינָֽן׃

My answer was as follows:

The alternation you are speaking of is between a zakef gadol (on the many, short names) and a 'pashta'-zakef katon (on somewhat longer words). Both of these are really a zakef. When the zakef comes on the first word of a clause, or of a pasuk, as it does here, then there is no place for the servus. This is where we typically see a zakef gadol version of the zakef.

The 'pashta'-zakef katon is caused by purely musical concerns, based on characteristics of the syllables. But it is really just an equivalent of the zakef. Here is what William Wickes has to say about it:

If there is a closed syllable in the word, separated by one or more others — or, at least, by vocal Sh'va — from the tone-syllable, an emphatic intonation (a high tone, as the position of its sign above the word implies) was introduced, serving as a forebeat ( Vorschlag) to Zaqeph, in the absence of the foretone. It was known as Methiga, being like an upper Metheg (comp. the use of the term in the accentuation of the three books, Taamei Emeth, pg. 70).

Keep reading at the link for more information about the Methiga. But consider: Le-Yis-sas(?)-char. That is a closed syllable, Yis, separated by one other syllable - sa - from the tone syllable, char. So too Bin, a closed syllable, ya, a separating syllable, and min, the tone syllable. And so too Naf, a closed syllable, ta, a separating syllable, and li, the tone syllable.