So I saw on ffxicyclopedia, but not on BGwiki that souleater is affected by species resistance. So I thought I would test and post about it to link as a reference for BG wiki. TLDR: souleater does get a boost from species resistance like +25% piercing damage.
I did my testing on Ogre Fly in The Sanctuary of Zitah where my attack is capped easily. If you saw my other post you would see I derived the Ogre fly def/vit/lv in area. These values are now on BGwiki, the data driving the decision on this test was from a lv41 Ogrefly.
I used NIN/DRK with a 29 base dmg dagger. Weapon rank = 3, so fSTR cap was 11 and reached at 80 STR which I easily surpassed with 200+ STR and 700+ Attack during the testing.
I had 2036 HP and I only counted the first hit, which would have been a 101 bonus to my damage.
Because NIN was my main the SE contribution was 5% and my dmg limit+ was 0.1 making the pDIF cap 3.35 with a range up to 3.518(with the 1.05 randomizer).
I first swung 10 times to confirm my damage without SE was in range.
(base dmg + fSTR)*pDIF*species = total
min = (29+11)*3.35*1.25 = 167.5
max = ((29+11)*3.518)*1.25 = 175.9
My swings were: 168, 170, 168, 171 ,172 ,173 ,175, 168, 172 so all good there.
Min/Max if souleater doesn't benefit from species resistance:
(base dmg + fSTR)*pDIF*species + SE = total
min = (29+11)*3.35*1.25+101 = 268.5
max = ((29+11)*3.518)*1.25+101 = 276.9
Min/Max if souleater does benefit from species resistance:
((base dmg + fSTR)*pDIF + SE)*1.25 = total
min = ((29+11)*3.35+101)*1.25 = 293.75
max = ((29+11)*3.518+101)*1.25 = 302.15
My first SE melee swing came in at 297.
Conclusion: Soul eater gets the species resistance bonus or penalty.