The numbers are arbitrary because its just a rough example and yes there are variables that are basically impossible to determine without reference to actual game states.
If you are lazy/dont have the time to do testing then you can simply work it out this way:
The nature of upgrades is that they are either relevant or they are not. You break it down to a binary equation.
For example:
ACD is only relevant if the Phantom shoots first, assuming that the player who paid for the ACD is using it for its defensive properties. If you shoot before the phantom the value of the ACD is now 0. Similarly the points paid for Whisper's innate ability and probably V.I as well would be negated. Therefore by shooting first you are basically stripping your opponent of 3 advantages and if you paid less than the cumulative points of those upgrades to shoot first then you have a huge advantage that will force your opponent to react to it or just straight up lose unless they are extremely lucky.
Every ship bar the Imperial Shuttle could potentially out bid Whisper for initiative either through straight up upgrades or through indirect initiative bidding. This makes a strategy dependent on ACD potentially hazardous and 'low value'. Which is why I am avoiding Phantoms as a list to take.
Bad example, bad math, or both. Regardless if a phantom shoots 1st AcD happens when it shoots and effects all choices after. Also, as it seems the development team has noticed, both in recent costing and in recent design, PS has variable return on investment. PS 3 is probably more important than 4 in today's meta but that was not the case 9 months ago. 4 mattered and 5-6 was "big"; now 3 is important, 4-6 irrelevant, and 7-9 key, and 10-11 is the new 6.
I don't understand your "numbers" and disagree with most of your premise, and I'm not a huge math guy. The game is built at 100pts. The farther you get from that, the less value any number has.