Yeah, changing the % value will change the numeric value (and vice versa). I'll check in a minute, but I think the "Equip All" is the exception to the rule. I think (but even thought it was only a couple of days ago, I can't remember!) that I made selecting "equip all" leave the other boxes alone so that you could easily revert back to your old value if you changed your mind. Setting 100% automatically selects "equip all", though.
As for 100%, that's equiping all of the unit. Numbers are in absolutes (from a minimum amount to either a maximum amount or the size of the unit, whichever is smaller) and percentages are proportions of the unit size (e.g. "up to 1/3 of the unit may have bows" in Lord of the Rinds).
WarFoundry will have preferences, but for now it doesn't have a preference panel. You can still hack the preference stores by hand if you want, but you've got to know what you're doing. Preferences will be used for several things, including alternate data file loading locations.
As for exclusivity groups, they're in as part of equipment the equipment definition rather than as restrictions. The most obvious place they're available at the moment is in required equipment where you can "replace" a required item with another required item of the same exclusivity group. The exclusivity groups in non-required items probably do need checking, but that's part of the beta test - finding things like that that I may have overlooked
The tabbed grouping is probably a good idea for when there is too much equipment, as it doesn't have to be exclusivity group-based. If you just have "weapons", "armour" and "mounts" then a character can have a sword and a bow (two weapon choices) as well as armour, a shield and barding. By categorising the equipment then it makes it easier to find what you want, it just wasn't a situation I'd considered before