While it's good that the breeder alerted you to the problem, I'd also be wary of taking on a dog with this condition without a thorough exam from a vet I trusted. Especially if the breeder can't answer whether this condition has been present in the parents, grandparents, aunts, uncles, etc. and whether it closed with maturity in those cases. I'd also be reluctant if:
1. The puppy was being sold at the same price point as its siblings with no obvious congenital defects
2. The puppy is being not sold under a contract that offers some kind of protection in terms of refund, help with vet costs, replacement puppy, etc. in case this condition requires extensive treatment, other congenital issues occur, or (goodness forbid) the puppy needs to be euthanized due to complications from this or other congenital conditions.
3. The breeder is not willing to take the puppy back for any reason, related to the fontanel or otherwise.
These aren't hard limits for me. For example, if the puppies were being sold for a relatively low amount to begin with, or if I felt the breeder was offering something exceptional that would be difficult to find elsewhere that justified the cost (not like breed or color, more like if the puppy had been through a rigorous socialization program and was already potty trained and crate trained, etc).
Now congenital issues can happen to the best of the best breeders of any breed. But what I'm saying is that if I'm going to be paying high quality breeder prices, I'm going to expect a dog that has everything stacked in its favor, from genetic testing on the parents to neonatal stimulation, socialization, and training. And lifelong support from the breeder for any training and behavior questions, genetic issues, or rehoming the dog if ever necessary. If the only thing a breeder can offer me at those prices is a cute puppy, well. Virtually all puppies are cute. Add in a condition that may or may not be a big deal, I'd be pretty hesitant. Rather just choose a cute puppy from a shelter or rescue at that point, or find a breeder whose practices deliver on the cost.