HopeW,
You'll get the best advice about whether you should have a transplant from doctors with the most expertise with MDS and lupus.
If your decision, based on their recommendation, is a transplant, and you are healthy enough and have an available donor, then the best place to have the transplant depends much more on a medical center's bone marrow or stem cell transplant experience than on what diseases you have. There are also the practical concerns of insurance coverage and the goal of staying close to your support team of family and friends.
The National Marrow Donor Program provides information and statistics to help patients
choose a transplant center.
It may be wise to have the transplant center that you choose do the BMT health evaluation, because they'll be evaluating you against their practices and protocols. The evaluation is likely to be a general health checkup and a full review of all health issues you have. They're looking for anything that increases transplant risk, for which they use the unpleasant term "comorbidities".
In many cases, doctors use drugs to try to bring an MDS patient's blast count down before transplant. It's a tradeoff, because they want to minimize your need for transfusions, and the longer they delay a transplant, the more likely transfusions become and the more there's a chance of a health setback.