The withholding has nothing to do with the RMD questions or saying you didn’t take the full RMD. The withholding will show up on 1040 line 25b.
Turbo Tax changed this year. When it asks about the RMD it is only asking for that one 1099R you are entering. On each 1099R you need to say Yes it was the RMD and only enter the amount from box 1 on that single 1099R for the RMD, not the total RMD for all and even if it is more or less than the total.
Until they fix it try Expert DavidD66 excellent answer here,
https://ttlc.intuit.com/community/retirement/discussion/re-rmd-mismatch/01/3488686#M234445
