Because i play on larger than earth planets, So that one rail line is gonna have to support a hundridish units at least, and at the dead minimum a dozen zones, could be as high as 30 zones per side. This can lead to problems with creating units on one side of the front. The economy isnt optimized, so that means that if i have one zone producing the metal another needs, it could end up sent back to SHQ, and then from their to my heavy industry in the next door zone. Limiting the attached zones with an SHQ minimizes this efficiency, and in the long run saves hundreds of credits per turn on infrastructure maintenance costs, and still allows me to specialize and make use of smaller zones that dont have the population to be self sufficient, which means i can keep creating more zones and expanding them internally when im not making progress on a war front. Rebellions are not an uncommon thing in such an empire when youve got so many leaders to be keeping track of, so if a rebellion on that rail line means my empire gets cut in half for even a single turn, it could mean the end of me. Id much rather a mountain path and wouldnt zone split for that. A thousand IP is easy late game, population and credits is the only real bottleneck.
I developed my strategy and understandings of the economy months ago so it could be my information is outdated on the inoptimal logistics ai, but even then i just cant bring myself to not have redundancies in the logistics network. WITE russian partisans have scarred me for life.
As I thought, this all has nothing to do with there being a 1-3 Hex wide Landbridge. So the conditions you gave for making a 2nd SHQ were not what you are actually using.