Regarding plugins, I think mifki would know better than me.
The vanilla petcap is per species.
Regarding minerals, in my experience you absolutely get more veins and gem clusters with more - I found scarcities past 135 increasingly likely to be worse for custom 1x1 embark, though I eventually decided the best was 117 iirc. (I tried to maximize rock crystals as a major priority, so ymmv, though I also eyed having nearly all metals in useful amounts). I started with 500s and 200s and then ditched them. With 100s, can get up to 6 veins per embark tile, with 500 you get 2-4.
(ex from my (incomplete) notes { 202 scarcity: 700 iron, tetrahedrite, 251 adamantine, 150ish galena, silver, sphalerite, 42 gold, 31 platinum, 9 bismuthine || 6/22/101: reanimating, husking fog, 33 casiterite, 67 gold, 21 rock crystals (if iron was missing would be noted) || 117: 193 kimberlyte, 4 diamond_fy, 6 diamond_fy, 2 ruby-star, 43 rock crystals‼, 500 garnierite, 1000 iron, 300 gold, 200 tetra, 200 silver/galena, 70 platinum, 13 cassiterite, gypsum, bitu, lignite, jet, cinnabar, base 78,67% coverage w/o ogres } )
However, when it comes large clusters you only get 1 per 48x48x1, and further minerals will just remove your precious magnetite in favour of gems, which you may find useless. What large cluster you get is basically random, though, if your scarcity can roll one - I think one of the gens I ditched had something like 4k iron, in a system where every sedimentary layer had a magnetite cluster. This sort of rng means that 501 scarcity gen can be superior in every way you care to a 100 scarcity one.
Furthermore, you get more uniform appearance of fortress by having less minerals - less gems dotting the natural walls.
All of the issues can be modded or scripted away (such as with geomanipulator), though.