I do note that the package at Buddy's included the 6 boat dives (which I assume are to get to Klein Bonaire, primarily) and unlimited shore diving. It is fair to assume these shore dives are "at your own leisure," which is to say you simply check out a tank or two and walk out into the surf?
If it's like it was when I was last there a few years back, it's like this. For shore diving at BDR, there are tanks available near the pier, and you can get one, gear up on a bench, walk out on the pier, down a ladder, then fin out to the reef. There was a rope running out to the reef, which is nice as a guide back in...including on night dives.
There was a separate place for tanks, IIRC, to be taken for offsite shore diving. I believe that closed at 5 p.m.? For air tanks, there was a drive through. For nitrox tanks, since you have to analyze them anyway, I just walked over, got a couple, analyzed them, and carried them to my rental truck.
What seems to be the customary directive is to take 2 tanks/diver at a time for offsite shore diving.
Bonaire is a good place to start doing some unguided (shore) diving, since the proximity to shore helps ease navigation demands and you don't have to be back at a boat at a set time. Since the reef wall slopes, you are usually diving over a 'hard bottom,' not alongside a vertical wall plunging into the abyss (which you may see in Little Cayman, for example...and is really cool).