Both of these water leaks damaged the kitchen base cabinets (brand new and installed in Aug 2017) resulting in moldly cabinets along the inside bases, damaged water resistance vinyl laminate floors in kitchen, damage to living room wood laminate floors, and a bedroom with moldy carpet due to leak from the the hole in bath tub.  

Not sure what I can do but seems I need some way to block the water from their roof or change my vinyl siding to something else.

We've put in click-type Luxury Vinyl Plank (LVP) and Luxury Vinyl Tiles (LVT).

He did provide a Scope off Work at the beginning of the project, but he never adjusted any of it for change orders such as substitution vinyl plank for carpet.

I'm willing to bet that your flooring contractor is charging per sq. foot which means he makes more money by doing it the easy way.I'll be doing a flooring job soon and the only place I will be putting the flooring underneath anything is in the bathroom where it will go under the toilet and vanity only because it would be virtually impossible to install the vinyl planks in the small spaces between them and the walls and the tub. 

Also, any other ideas outside of the typical carpet, carpet tiles, tile, vinyl rollout/plank, etc would be welcome to research more.

Vinyl flooring will usually peel up easily near the shower/tub if it's leaking.I'll try to poke my head in the crawl space if there is one.

Vinyl siding is definitely lower maintenance, but a good paint job will last many years as well. 

Rewire, refinished hardwoods, new countertops, new paint, added a bedroom, put vinyl floorings in apartment.

  *  I would use Vinyl Plank flooring - not laminate*  I would also not use granite, unless your market dictates it.