I agree with Beka, it makes a lot of sense. Think about it: a water bottle puts out the same amount of water per lick no matter how big the rabbit is. That means that for a Flemish giant, he would need to make 2 or 3 or even 4 times as many licks to get enough water. I am not sure how much water a rabbit gets per lick out of a bowl, but my guess is that it is in relation to rabbit tongue size and appropriate/proportional to their body size. Basically, it gets them the amount they need.
Now lets look at a regularly sized rabbit drinking from a water bottle, they already spend a lot more time getting water than a rabbit that has access to a bowl. In my observations at least, it seems like a rabbit getting water from a bottle will spend about 30 seconds getting water compared to the 5-10 that a rabbit drinking from a bowl spends. That tells me that one lick at the bottle is certainly not equal to one lick from a bowl. Let’s assume that for a normal sized rabbit one bottle lick is half as much water than from a bowl lick. If it takes the Flemish just twice as many licks as a regular rabbit, it could end up spending a whole minute trying to get enough water. For me, spending a whole minute trying to get water out of something when I was really thirsty would be very frustrating and I might give up after I have had just enough to wet my throat. This could lead to chronic dehydration, which causes all sorts of problems, particularly regarding calcium excretion.
On top of all of that, the breeder has basically told you that your boy has never been introduced to a water bottle, and is only used to drinking from a bowl. So he would not only have to learn how to drink from a bottle, but it is a transition to a less efficient water delivery system.