CUHK and ZDIC omitted this chemistry meaning. So did ABC Chinese–English Comprehensive Dictionary (2003), p 1134. I can't access the "slightly revised through July 2005" ed.
Isomer is "同分异构体", which briefly written as "异构体".
"异" emphasizes the "slightly difference" of the arrangement of the atoms.
"同分"(same number/type of atoms, and majorityly same arrangement) is often omitted, so "iso-" is "异(異)-". For more types there is "新-".
Some other examples like "顺(順)-" and "反-": 順-2-戊烯/反-2-戊烯, 順式脂肪/反式脂肪.
This is my guess.
Methane, ethane, propane have no isomers. Butane has two isomers. The straight chain one is called normal butane, thus, n-butane, and the one which has an additional methyl group (not counting the main chain, the three-carbon propane chain) at C2 is called isobutane. Normal is conveniently translated into 正, the other, being different from normal or 正, is called 異. The naming emphasizes it's different from normal. This is in sharp contrast to its English name, isobutane, which emphasizes it's an isomer of n-butane.
When it comes to pentane, there is a new type of isomer in which C2 has two more methyl groups (again, not counting the main propane chain) bound to it. This one is called 新戊烷，新 implying it's neither 正 nor 異 but a new type of isomer.
That's my guess. In fact, I have never been taught the etymology of chemical names in school.