There is no mention about stem cell transplants in WTS publications. But I found these comments.
https://www.ncbi.nlm.nih.gov/pubmed/29795417
Tandem autologous transplants are generally the preferred therapy for newly diagnosed intermediate- and high-risk myeloma patients. More Jehovah's Witnesses (JW) are receiving single autologous peripheral blood stem cell transplants (PBSCTs). However, tandem autologous transplants have not been reported in JW patients.
http://www.bloodjournal.org/content/124/21/3976?sso-checked=true
Autologous Stem Cell Transplantation without Hematopoietic Support for the Treatment of Hematological Malignancies in 125 Jehovah’s Witnesses
High dose chemotherapy (HDC) followed by Autologous stem cell transplant (ASCT) has been shown to provide curative benefit in patients with relapsed lymphoma and multiple myeloma, often times requiring hematopoietic support until marrow engraftment. Due to Jehovah's Witnesses (JW), refusal of blood products treatment challenges arise.....(the rest of the article is an explanation how to treat jws)
There are many
more articles with a good search "Can jehovah's witnesses have a stem cell
transplant"
----italicized part is probably why jws can take it as cell as from a single lot from the patient being treated.
The primary difference between allogeneic and autologous are the source of the cells for the therapy. Allogeneic therapies are manufactured in large batches from unrelated donor tissues (such as bone marrow) whereas autologous therapies are manufactured as a single lot from the patient being treated.