Currently, optimal strategy typically involves queuing up dozens or even hundreds of comsats at each border system, letting them build 2/3 of the way, and then leaving them on the bottom of the queue, ready to pop out at a moment's notice, should invaders approach. This is a tremendously cheap insurance policy that greatly extends the staying power of defenders and planetary weapons and makes invasion extremely expensive.
The OP's proposal at least has the virtue of making this cheesy strategy no longer be viable, which I would construe as a move for the better.
However, I think that there are likely even better ways of solving the decoy comsat problem, e.g., by reducing the targeting priority of unarmed troopless decoys. If some other solution like this can solve the decoy problem, then I think the game would benefit from reworking the "upkeep" system to one that charges more for big ships than it does for little ships, thereby making it more viable for players to use smaller ships later in the game. I suppose that sort of change in the upkeep system could also be paired with charging upkeep for partially constructed ships (or perhaps on whatever percentage of them has already been constructed).
But overall, charging upkeep on ships under construction feels to me mostly like annoying complexity that doesn't serve a real purpose, and Free Orion's design philosophy rightly avoids such things! If you *really* want something like this, I'd probably go with Krikkitone's suggestion that ships that aren't being worked on should have their PP decay -- either keep the project going or pay more later to get it going again.
For what's not in 'Top Priority Game Design'. Post your ideas, visions, suggestions for the game, rules, modifications, etc.