Kizaru was fighting 4-5 pirates, thus he was in "combat-mode". Consequently I believe he already had his logia switched on. About that music, Im not saying he was expecting to be attacked by music, but I believe he was expecting to be attacked in
any kind of way. Though doesn't matter, since he probably was the whole time in "logia auto form" (damn we need a official word for that.. xD)
About ur second part of past, I do understand what you are saying. But I believe you are making it too complicated. I think it is more easy.
Here Kizaru is attacked by a bullet, which hits his physical body,
as u can the see the smoke on Kiz's neck. So even he must be aware, but in this case, he didn't bothered to switch, since those guys were too weak.
About BB vs Mwk, BB can surety take at least on hit from Mwk. If u are thinking he would go down by just one hit then u are terribly underestimating him. Though I agree, at this point I can see him only in disadvantage, same with BB vs Kuma.