At 46 degree water temps, I'd probably leave my feet in the straps for extra warmth.
But that's not helpful. Sorry.
I am a fan of neoprene dive socks, too, and very loose straps. Honestly, with 5 ml booties, I'm not surprised you have a challenge with your board offs. Combined with a thick wet suit or dry suit, it's gotta' be hard to make 'em happen in the colder months.
A larger board handle might possibly help, because you don't have to be quite as limber and flexible (which is difficult in winter gear). But if it's just about the feet due to increased size and decreased sensitivity from 5 ml booties, you might experiment with modifications to your foot-straps to make them larger. I haven't done this, but I may.....I'm always at the maximum size setting on all my board straps, and another inch or two might be helpful for quick entry at the end of a board-off. An extra piece of velcro or two on each strap might make re-entry easier in the booties.
Good luck, and let us know if you come up with a good solution.