Former pros can play D2 ball. Not sure about D3. D1 is ruled out.
As to lesser bonuses, they do occur. With the last collective bargaining agreement, a lot more teeth were put into the "slot system." Although the slot schedule amounts go up each year, you don't see as many outliers as you once did.
You do see guys get below slot. Most commonly this happens if they stay in college until their eligibility is exhausted, as that leaves them with no negotiating leverage with the team that drafts them. (Hence the willingness of so many guys to forgo senior year to take a pro deal after their junior year; that senior year can become an expensive proposition.) Other below-slot deals can happen if a player has something previously unknown turn up in a physical.
Also, some MLB teams are just more stubborn in negotiations than others. This is why some agents try to steer some players away from some teams.