I'm unclear what you are proposing happens to the vagina in trans men (I'm setting aside the needs of NBs for this) depending on the level of medical or even surgical intervention.
In the scenario outlined, it's plausible for a woman
—to take cross-sex hormones
—to retain the female reproductive organs and have a phalloplasty (iirc, healthcare systems in countries like Japan insist on the removal of the reproductive organs but other other healthcare systems don't) (second consideration is that phalloplasty can occur but the 'replumbing of the urethra' can take place in a separate, later surgery, if it happens at all because some may be content with the aesthetics of the neophallus and it is accepted that the urethral hookup is associated with a number of complications to an estimate of 50% or more).
Then, either a natural conception happens (not uncommon) or it happens after pausing the cross sex hormones (intentionally or not).
Conception might happen naturally or in an assisted manner as I outlined above which may be DIY 'turkey baster' or PV sex because the vagina etc. still exists even if the vagina may have some degree of atrophy. (Prof Susan Bewley highlighted that it would have been useful for the workbook in the OP to have discussed the feasibility of vaginal birth if the vagina is atrophied because it may not be capable of sufficient dilation and may tear badly. Presumably, if the conception is planned, there would need to be extensive shared decision-making around the elective Caesarean if necessary. If the conception is unplanned, then much might depend upon how much prenatal care has happened to be able to prepare someone for what may happen.)
Depending upon the personal circumstances or the level of need, the assisted conception may be via a clinical intervention.
Notwithstanding all of the above, I should think that the number of people presenting to a midwife with internal female reproductive organs plus a phalloplasty with urethral hookup will be very low but I may be very wrong.