Yeah I use Twilight Menu++ too and can't heal outside of battle. You just have to work around it I think.
Yeah, it's not too bad, really. I mean, I do tend to use it in most other RPGs after battle to bring my party back to up to snuff, but it works here. To be honest, though I did find an accessory that boosted my MP quite a bit, the characters in general don't have a lot of MP to work with anyway, so either way I'm having to revisit the save stones fairly often when grinding.