Now here's the harder concept to understand...
Each box is not worth the same.
Consider the F-DD vs, say, the I-DD.
Both have Ph-1's. The I-DD has 4 phasers making a "proper" Ph-1 loadout for a DD, ie, 1/2 the I-CAs load. The F-DD, meanwhile, has 6 Ph-1's, which is 2/3rds the CA's load.
Then there's weapon arcs to account for. Granted, all phasers on both ships are 180 degree arcs. Feds are arrainged 2X FH / LS / RS while the ISC has 2x LF / RF. However, their coverage is much different.
The ISC can only bear it's 4 phasers at a target in the FA arc. The Fed can bear 4 phasers at any target throughout it's entire FH arc, along with 4 phasers down the rear centerline. And, to top it off, depending on the weapons marked as destroyed, it's possible for the Fed to still have at least 90 degrees of 4 phaser coverage (from Front Centerline to undamaged side's side centerline, for example, mark both LS phasers as down the Fed gets 4 phsers from Front Centerline to Right Centerline), while losing even 1 phaser on the ISC ship results in the inability to provide 4 phaser coverage. Also, the ISC has no RA phaser coverage at all, while the Fed gets 2 phasers covering their tail (4 on centerline).
So, considering all this, you can't just flat out tell me that a Ph-1 is a Ph-1. SVC himself admits that values for "identical" boxes fluctuate based on arcs, number, coverage, expected amounts for typcial opposition, etc.
Taldren didn't take this into account, and they assigned a flat value to each box. I'm willing to venture that each box is actually worth more than what Taldren assigns to them, hence the leftovers on the health bar when a ship is destroyed.