I must agree with several of your comments - and especially the observation that the suitcase might have been traced back to the R's if it turned up with a body in it. But couldn't that have been explained away by suspecting an intruder found it handy there in the basement, so why not use it? All the more reason to try to direct the blame to kidnappers, IMO.
But, as you say, the plan might have included using the suitcase to dump the body, then returning the suitcase. Deciding not to use it, but leaving it in the train room makes as much sense as any other explanation - especially more sense than an intruder using it as a "step" to get in/out of the window, when there was a chair not far away, which wouldn't have been nearly as wobbly!
Yes, they could have blamed the "kidnapper" for the use of the suitcase.
At any rate, we know the suitcase wasn't used in the crime, as the body was never dumped. It may have been considered as a vessel, or maybe not. The duvet may have been considered as something to cover up the body, or maybe not. We don't even know that it wasn't cross-contaminated; BPD didn't exactly run a professional crime scene investigation.
Basically the suitcase can't tell us anything. We won't solve the crime by analyzing every detail about it. The fiber evidence is meaningless. Why a college boy has a duvet and a Dr. Seuss book in his suitcase is pure speculation. Nothing much to be gained from delving into the suitcase, IMO.