There is one thing that kinda confuses me - does this mean that the Jolla has a custom made battery ?

I would kinda expect them to just use one of the off the shelf ones or those used by big smartphone manufactures, which should be easily & cheaply available from first or third party sources. It was like this for the N900 (it shared the same battery type with other Nokia phones) and I'm sure there are many other examples.

Or is there some really important specific reason why they would need to roll their own battery with all the possible drawbacks (limited availability, dependency on supplier/tooling, price(?)).

"We can make more money by using battery that is not compatible with anything else and can be bough only from us." <- Is the only thing I can come up with, but it does not sound very convincing, considering Jolla is still not selling replacement batteries 9 months from launch.