Train in whatever you feel comfortable with - pays your monies, you takes your choice.
Just remember that the gearbox shouldn’t be the ultimatum; good quality instruction, correct vehicles & facilities (i.e. private DVSA test centre) would be at the top of my checklist.
Having learnt myself in a 4-over-4 box (and now operating a fleet of fully automatic vehicles for training purposes), it would be a no-brainer for me. IMHO, it’s easier to learn the use of a manual gearbox once you relieved the pressure of the practical test; it’s one less thing to worry about.
Hope that helps.