Personally, I think that they thought everyone would believe their burglar story. I mean, just looking at it from an layperson's perspective, not knowing the evidence in the case, it is much easier to believe that a burglar would have come in and raped and murdered Meredith, then to think that oh, 3 people played a prank on Meredith and something happened, and then 2 people came back and cleaned up the cottage and cleaned doors and moved the body around to stage it and staged the window to make it look like a burglary, etc., etc.. Just like from reading this thread, one can see similar things being said from some of those supporting her innocence, even knowing the evidence. So of course a layperson is not going to automatically think the second thing, they are going to think the most obvious thing - the first.
The problem is, they were thinking of it like how a layperson would view it. They didn't count on how investigators would see it. Investigators who are familiar with these things. They thought someone like you or me would look at it from a very cursory view and think, well, duh, a burglar came in.
I posted an article on last thread where the author said that most of the times during staging, perps make mistakes because they don't think of things in terms of the way detectives and investigators will see it. They think of things in terms of how a regular person (not in crime investigations) would see it. That's where they make the mistakes.
So I do think that they were thinking that investigators would buy the story, especially given they had staged everything to make it look that way.
As far as Rudy goes, I think that they thought that perhaps the investigators would not be able to match anything to Rudy. I mean, how would investigators have known Rudy was even there? Maybe they thought that since Rudy would not be on the radar for this murder, his DNA would not be taken, and thus they would not be able to match it. I think that they just wanted desperately for investigators to believe in the IDEA of the "burglar."
I think their back-up plan in the case if Rudy was ever matched and found, would be to deny deny deny. That who would believe some Black man over them? But I think this was only their back-up plan in case Rudy was matched and caught, which I don't think they actually thought that they would be able to match the DNA with Rudy.
The idea of the burglar is what they wanted to be believed.