Are rear derailleur cable intervals equal?
Your assumption is that there is an unlimited number of clicks in the indexing inside a shifter. There aren't. For rear derailleurs shifters there is one click for each gear in the cassette. (i.e. a 10 spd shifter has 10 clicks). If you mis-align the clicks, you only get 9 gears not 10. 

Often the indexing is setup to pull a larger amount on the biggest cog ( or lowest gear) in the rear cassette. It's tuned by the manufacturer to get the best shifting performance based on the typical cassette used in the group. 

I suspect the issue from your older bike was not due to indexing, but due to a worn cog in the cassette. One gear in the middle just being flaky is a common symptom of a worn cassette and chain. 

Cogs don't get the same amount of use or force through the chain so they often wear at different rates, especially if you don't replace your chain often enough. If you want the best shifting, get a chain gauge and check your chain for wear at regular intervals. My strategy is to buy the cheapest chain that works and replace it often.