Can someone explain stroker kits

A stroker by definition just has an increased stroke vs a stock engine. Bore size doesn't necessarily have to be increased, however most of the time its a byproduct of a rebuild.

As far as "why didnt the factory do this" in many cases they did. Most "engine family's" are just different bore and stroke versions of each other. In gm land this how you get everything from a gm 302, to a sb 400 from the factory using essentially the same block with just varying bore and stroke. In sb mopar comparison, not a huge difference in a 318 and a 360 other than bore size. You can "stroke" a 318 to a 390, just like you stroke a 360 to a 408. Bore size being the difference. Both with a 4 inch stroke.
The late model hemi's are pretty much the same example. The 6.1 and 6.4 are essentially bigger bore and stroke 5.7's.

When building from scratch, your thoughts are correct, there is little reason not to go with a stroker assembly. Cost is usually negligible when your purchase includes a new crank.

To get a stroker, the crankshaft is designed with more stroke, and the pistons are designed to have a different pin location, so they stay in the block when at Tdc.

408 is the common mopar sb stroker, and they are every bit as reliable as any other rebuild. The crank is just a 4 inch stroke. The only disadvantage I can really stretch to list is that pistons moving further in the bore have higher stress. Due to moving for a longer duration of time in the bore, before changing direction ( inertia ). This is why some big rpm engines are actually "de-stroked" ex. The hellcat is a 6.2 opposed to a 6.4, or a chevy 302 engine vs a 327
Thats my quick and dirty explanation :)