Yeah, splitting out the full attacks into single attacks is virtually impossible to automate and get right 100% of the time - due to feats and creature special abilities and, especially, natural attacks. You can't just apply a blanket +5 This is really all down to how Paizo present their statblocks.
However, the Otyugh example is correct: the tentacle is a secondary attacks, so even a single tentacle attack would be made at -5 for the secondary attack - resulting in -4 with the weapon focus. So this is correct as listed.
Details on natural attacks here:
https://paizo.com/pathfinderRPG/prd/...atural-attacks The information of interest is: "Secondary attacks are made using the creature's base attack bonus –5..."
As such, a lot of statblocks that have natural attacks work out correctly. It's when you have two weapon fighting etc. that problems can truly exist.