What about splitting upgrade points up by technology line. So my Spire tech points only work on Spire modules. Give some of each when you level, possibly weighting the points towards the ship type you are using when you level. The total number of points available would be higher, but you'd still only have the original amount of points available in any given ship line. For example, say you got 5 points when you made a level now: you'd get 3 in every tech line under this system, with maybe one extra point based on the ship type you are using (13 total).
In addition, maybe Mark IV and V unlocks might require 1 and 2 points respectively from each other tech line, so whichever ship line you push for IV+ modules on will draw points from the other ship lines, effectively giving you your "final" ship line. This avoids locking you in to ship line until you can see what modules you will have and gives you the option of not specializing in one line and getting multiple lines loaded down with Mark IIIs.
Basic modules might have their own line of points, or simply require points from all lines. Another option for them is to make them auto-level up to Mark III with nebula completions, and let you upgrade them to IV+ with a much heavier multiple tech-line point investment.