It sounds like you have some questions and also some criticisms. I'm sure these guys are professionals and this topic is not so cut and dry like say mathematics. So this community is going to be more used to this sort of thing I think.
If you're worried you might offend them, maybe you can ask them your questions and at the end, offer them the critique. This way if they don't want that, they won't request it. To me this seems logical as you get to ask your questions, and if they don't care to hear any criticisms on their paper, they can opt not to ask for them. Not to mention, it saves your time writing this part, which could go wasted if they simply don't care.