For most things cylindrical cells are the right answer. They don't puff up, they're available with protection circuits, they're cheap and highly available, you can get them in a variety of sizes and capacities, even in different chemistries.

Using a custom cell might make sense if you are making a) one megakajillion of a thing or b) you have extreme volume limits which mean you're probably using a pouch cell.

In HW engineering, Not Invented Here syndrome costs you big money. You have to have an actual business case for re-engineering something that already exists plus the capital.

95% with my stuff of the time COTS cylindrical is the answer, which means my shit comes in on budget.