I think it's pretty likely that Boo began to craft his plan once Gotenks informed him about his diminute time with fusion. We see that Boo, while laying on the ground, makes an expression of worry and seems visibly annoyed once he gets up. I think this is all because the information given to him by Gotenks changed the way he should operate. Atenting to details, we see that Super Boo broke that hourglass at the lookout more or less at the same time Gohan showed to be pissed off by Old Kaioshin's method and subsequently powering up, which could indicate that at this time Super Boo shifted his attentions to a warrior that might surpass him. He seemed more emotional due to it.
When fighting Gotenks, it's notable that the fight seemed pretty evenly at first, with Gotenks maybe getting a minimal advantage with his special technique that trapped Boo and his barrage of chi blasts. Then occurs the sequence described above in which Boo's annoyance could stem more from the revelation that Gotenks has a time limit, rather than fighting someone of his equal as Piccolo guessed.
He then knew that killing Trunks and Goten after the fusion ran out would serve no benefit given he needed them to best this still unknown warrior. I think that is the moment referred to Boo as him staling and letting them live until they served their purpose (I've seen some ppl, mostly from the Portuguese forums I firstly began frequenting, arguing it means Super Boo was staling in the very fight against Gotenks, which isn't a necessity).
Boo acts as Gohan is the first warrior to have surpassed him, but since Gotenks isn't on a different level from him, enough that the fight isn't a certaintity due to Gotenks' limit time, I think placing the emphasis on someone who noticeably surpasses him with no burden of time makes sense.
I like the logic you first brought up in your OP (being already a point I had thought about long ago), and it makes sense as if he were capable of besting Gotenks, the boys wouldn't be as willing to fuse later on. But still, I'd argue that if such was the case, Boo would have better reflected it on his dialogue later on against Gohan. Plus, also worth noting that Gohan seemed fine with Gotenks initially taking on Super Boo once he saw him as a SSJ3. I think he would have noticed it if they couldn't get the advantage against Boo.
Not saying it can't work, although I find it less likely than giving Gotenks a small but noticeable advantage, like 1.1x~1.15x.
