Well, for one, it allows for more stacking options at high PR than what "high build rate" ships have to offer.
There is a reason why high planet empires can successfully spam pure capitals to survive, often for months on end:
Such spams have the highest success rate for the amount of turns it costs, and if you lose your losses are decreased and your recovery from a loss is faster. With a balanced fleet, you could conceivably be wiped out by another equally balanced fleet, esp if you attack on normal or aggressive. However, with capital spams on careful (or normal if you`re feeling lucky and wana go for the 2 planet score), you`re not going to be wiped. Even when you lose badly, it doesn`t cost as many turns to rebuild.
The reason why a "balanced stack" is risky for high planet empires (particularly those in bad need of borders):
1. A failure is expensive in terms of turns, whereas a failure with a spam is not as costly.
2. You can only go so high with a proper balanced stack, whereas spams allow you to go much higher much faster.
3. It`s simply not as efficient, esp when a specific spam can easily and effectively destroy what amounts to hundreds of turns worth of ships.
All these discourage stacking for high planet empires, esp at a high pr (above 3 million PR). And if spamming works for high planet PR empires, it certainly works even more for empires with a lower base PR. Therefore, in order to encourage stacking, you should decrease the number of turns it takes to recover overall if you happen to lose.
I`m not sure how this would endanger the relative balancing of the smaller ships, since the stats would still be the same. All this would do is expose any balancing problems that already exist among the smaller ships, if any.
Of course, the "more work for the admins" is always a problem, but then again this could be used as an excuse not to implement any new ideas ever.