No you're the one who doesn't understand.
Crow had TJ mid August. You're looking at around 12 months rehab and could easily be milked for longer. That will likely push the Rule 5 roster time requirement to 2025. Yes he will need to be on the 26 man for 90 days before being optioned in that scenario but he's going to added to be added to the 40-man next offseason either way. So in regards to 40-man flexibility the only difference between Rule 5 and the trade is him being on the 40-man this offseason. In season he will be on the 60 day-IL which will take him off the 40 man. Next offseason he would have been added either way.
Edit: Before you say he won't be added to the 40-man next offseason we literally just added Bradley Blalock to the 40-man this year coming off TJ and never having pitched in AA.