Don’t be afraid to leave a little room in there … with this style of bike: longer wheelbase, relaxed geometry etc it actually makes sense to want the extra room as these bikes were designed to ride with fatter tyres and handle better for it. Also keep in mind that clearances on the front (fork crown) and back (brake and chainstay bridges) may be different so check both front and rear.
It’ll be trickier to load the bike on roof racks if they hold the bike without a front wheel, and it’s not easy to throw it into a small hatchback like a bike without fenders. Running more clearance is helpful if you’re wheel gets dented and you need to ride it home. 5mm between tyre and fender looks great … a little more is better, but not too much or things get caught up in there and it doesn’t shield the rain and dirt as well.
Really long at the front (in front of your feet) is preferable … many people make/attach an extra mudflap as that’s where most of the water/dirt on your feet and drivetrain comes from.
Plenty of info on the webs for fitting fenders and here’s a good write up form an Oz coolio …
Australian Cycling Forums • View topic - Velo-Orange polished fluted alloy fenders