After working on Serbian (T178926/T192395) and Slovak (T178929) and looking at the papers they were based on or translated from, I decided to reconsider what counts as "implementable" for Malay, and review the papers on Malay stemming and compare it to the existing Indonesian analysis.
My understanding of Indonesian and Malay was pretty simple, and that they are "more distinct than American and British English, but less distinct than Spanish and Portuguese". Also, Malay and Indonesian didn't interact in my investigation into fallback languages, where each is used as a fallback language for other languages.
However, looking at the wiki page on the matter, and reviewing some other sources, it seems that a lot of the difference is in Dutch-influenced vs English-influenced spelling of certain sounds, Dutch vs English loanwords, other vocabulary differences, and some pronunciation differences—all of which can decrease mutual intelligibility—but the grammar of the two standard forms seems to be essentially the same.
I also compared the Malay stemmer papers with the Lucene Indonesian stemmer implementation, and verified that they are working on similar affixes. There are some discrepancies, but the core affixes are the same, and the differences seem to come down to what affixes to try to account for (some derivational vs inflectional).
While it's possible that spelling differences or vocabulary differences could increase the error rate for Malay vs Indonesian, it seems to be worth testing; if it is successful, all we need to do it configure it—everything is not only already built, it's already installed, too!