May be others will chime in later in case I missed something, but here is my take:
My 90 day count date started from the time my case hit TRANSPROC. However, there is no set Yes or No answer to your question, due to AR 635-40, chapter 4-24 "Disposition by USAPDA" not having a specific timeline.
After asking the same question when I went through, the best answer received was: be flexible, have a plan A&B, have some adjustments on your part because the start day count down for NLT 90 can start from the day you signed the DA 199 or it can be the day you hit TRANSPROC.
Below is my timeline for comparison:
-22 SEP-signed DA 199 (demand FPEB)
-3 NOV-withdraw FPEB
-19 NOV-hit TRNSPROC
Good luck
T-man