If you're constipated then yes, it will make a difference. Basically if you have a mass of poo sitting right where you plug the substance a lot of it will just go into your feces and will never make it to the blood stream. For me this is a plus though because it means I can't plug every day and have to take breaks so I can have a few bowel movements between doses (so it keeps my use in check basically).
I think that's the problem a lot of people have when it comes to plugging, they try it one time and it doesn't work because they were constipated and they never try again. Even when you're totally cleaned out you can mess it up.
For example, I see a lot of advice here from people that say they jam the entire length of a 1ml syringe up their bum. That is totally not necessarily and is inserting it _way_ too far up there. You only need to go in just far enough to be able to squirt in the liquid without it dribbling directly back out. This sweet spot takes trail and error to find, but by your third time you should be able to find it with no issues what so ever.
The BA will vary from substance to substance like all other ROAs, but even those numbers seem a bit off sometimes. For example, some of the numbers I've seen for morphine are just slightly higher than the oral ROA, however, when I plug morphine it hits me harder, gets me higher, and lingers around for at least two days. If I did the same dosage orally I wouldn't even feel it...