Submissive Piddling / Assertive hand-nose tossing

Question
Our dog is a rescue - mix breed "Beagle-Whippet" per the shelter - 7yrs old? - male.  We have had him about three years.  We think he was abused/hit and punished with water.

He still on occasion will cower, ball-up and pee if he is startled or feels he is being scolded. Most of the time now, it is also when he comes in when we come home. The same dog will shove his nose under you hand and toss it to his head for "pets".  

I am wondering why he does these two seemingly conflicting actions.  

I have never heard of a submissive-alpha. :)

Answer
Yes this is unusual-but not unheard of,in fact this is more common in dogs that never been trained,because there used to running everything,and don't know what to think when there not in charge anymore

Enroll him in training classes won't hurt if you haven't done so yet-you can always teach an old dog new tricks