First off, hi and welcome to the forum 
Second, that sounds more like an exploit than a style of play! And I'm fairly sure you only get the "limited engagement" recovery if you win the engagement; it's a mechanic meant to prevent an exploit where you'd deploy a frigate, retreat, and have the enemy ships suffer the full CR cost for deploying.
Yo! Thanks!
And yeah, it would be an exploit the way things currently are, but there's a good argument for tweeking things so it works.
As it is, there's no benefit for being cheap and less capable. You do spend less supplies deploying, but you die more, too, which eliminates the bonus and adds crew loss to the cost as well. So the reduced supply expenditure is pointless : you can't draw the battle out to punish the opponent on endurance. Longer peak operating time doesn't work, that just punishes the player. Worse yet, the missile dependent hulls don't benefit from having all combat in one, long apocalyptic battle. You may as well beef up the stats and make all the ships more or less in line based on capability.
However, we can make it work. From what I see, you can just count a clean disengage as denying the AI from getting a limited engagement. This gives the player a chance at building a cheap, low-tech fleet with a small wing of dedicated assault craft to engage a superior fleet and try to pick away at it until the less robust high-tech fleets begin suffering from CR degradation. Missileboats also get to reload between fights, so it's an all around bonus to low-tech fleets.
The disparities in the tech levels have always bothered me, as I rather like the low-tech ships in general. However, giving them more tech to accommodate just feels like making low-tech into midline or high tech. We can actually shift the tuning over to logistics and keep the ships themselves exactly as they are.