Tested with Checker_Magga
Running Skill: 14.95
Combat Skill: 25.20

1) Small animals now ran away when I went close to them. So now they act as intended.

2) A Mule Deer in zone 863, x510 z714 was able to attack me through a limestone wall. Maybe you could reproduce it if you check these coordinates?

Some of the animal names confused me a bit:
Adult Veteran Male Golden Retriever Pup (84 hp) => adult, veteran, but still a pup?
Senior Greater Female Mule Deer Fawn => senior greater fawn?
Elder Veteran Male Pine Marten Kit => veteran kit?
Young Adult Lesser Pullet (8 hp) => adult pullet?

I approached an Adult Lesser Rottweiler Bitch (69 hp), it turned towards me, then went close to me but did nothing else. I walked away, it still followed me very close (Reaction: Go To Target) and while we walked a bit more the reaction "go to target" kept unchanged all the time, but the aggro increased slowly until it was very high and the Rottweiler started attacking. Is this behaviour as intended?