There have been several articles that have reported a correlation between high ferritin levels (ie iron overload) due to a high number of RBC transfusions and poorer survival with stem cell transplants. Here is an article that specifically discusses MDS and AML with transplant.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833064/
The article says that there has been a correlation, but that the correlation may have complicating factors, meaning it may not really be the transfusions or the iron, but may be the condition of the underlying organs, which may be more susceptible to infection and stress due to lower hgb levels over prolonged periods of time.
This article contradicts the prior article by saying that age was the primary determining factor:
https://www.ncbi.nlm.nih.gov/pubmed/22540302
And here is one more with thalassemia patients that is both recent and seems to suggest that iron overload can be managed.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451671/
I would say that with new drugs, treatment regimens, and awareness of different complications, that the state of the medicine has been changing, and it is possible that what your doctors and transplant teams are working off of is different than what may be available for reading by patients.
It sounds like a great question for your doctor and/or transplant team to see how they would manage it in the future.