I have a 52cm El Clem, aka Clem L, with bullmoose Boscos. I also have regular Boscos on my 26" Santana tandem. I use stem shifters on El Clem and bar end shifters on the tandem. I haven't experienced any knee hits, even when standing and sprinting for the line. (Okay, standing to power up an incline).
Sounds like you are still in the process of building the bike up. If that's the case, it can be hard to estimate this kind of thing by just turning the bars and noting how close they get. That's because the bars rarely turn that much, except maybe at really slow speeds--that's the reason toe overlap with the wheel is generally not an issue until you are putting along.
If they do hit, you have options. You could cut down the bars as necessary to prevent the issue--this kind of makes sense on a 45cm, in terms of being proportionate. Or you could go with an on the bar shifter, or stemmies. Or you could switch to bars with less back sweep.