I'll simply say this. Toon-up gags do miss on occasion. The idea of holding back toon-ups until someone is half way down is based on the assumption that the toon-up gags will work every time. Like any gag, they are prone to failure. Sure, you could fire off a unite, but you need those a whole lot more during the CEO fight itself. There is always the possibility that a last round toon-up, during which some could be hurting a fair bit if toon-ups are withheld during most of the battle, a toon-up gag could fail, and now you have a group of toons going in at a disadvantage. Or during an earlier part, the gag could fail, and we all know from experience cogs do not always spread out their attacks. They've been known to pick a toon and relentlessly attack. If someone's in bad need of a toon-up, there is the chance they'll go sad.
Now, am I saying that people are wrong to follow this strategy? No. If it works for them, all the power to them. I don't happen to agree with it, and thus I prefer to give toon-ups when they're needed. Is that fear? No. It's self-preservation, and a desire to see that the entire team makes it through with the best chance possible. I'll re-iterate my statement that I am firmly of the belief there is no 'best way' to play the game. The way that ensures that everyone enjoys themselves is the 'best way'. It's as simple as that. Many of the accepted strategies have been formulated around certain gag tracks being present. However, there are some toons out there who have chosen not to take those tracks, and they are more than welcome to do so. If that choice wasn't a factor, then we'd have all seven gag tracks instead of having to choose six. Therefore a different strategy is required to compensate for their different gag arsenal, and I find sometimes that doing a factory, or a mint, or a DA, or what have you using a variety of different strategies to be fun, and helps to take the tedium out of some aspects of the game.
My $0.02, your mileage may vary, cannot be combined with other offers, satisfaction not guaranteed.