Product designers can't just pick a standard and stick with it. Also, there are different applications for the same cells.
A few seem to design products for use with flat top cells, perhaps to save a bit of height on the product. Flat top batteries are more conducive for use in multi-cell battery packs.
Button top cells are standard for most consumer product use. The button top is added before wrapping it, I believe.
I would not advise trying to 'stack' flat top batteries, they would not make good contact, and it would be unsafe. Some use magnets as a 'button' to facilitate stacking them, but it's less safe than using button top cells, as the magnet can shift.
Button top cells are designed for stacking. The button makes good contact with the next battery, and keeps the thinly-wrapped negative shell a bit away from that contact point.