All of the photos seem to show (what looks to me like) granite or quartz countertops, wood or tile floors, and replacement cabinets (except for one, which had nicely refinished  vintage (mid-century) cabinets.

I am wanting to know if I could make the sides out of wood and cover them with hardie backed board (concrete board typically used to attach tile on) to protect wood frame from getting to hot and catching fire.

New kitchen cabinets and counters at Home Depot, new vinyl plank floors, new 3 piece bathroom kit, new tiles, new vanity, new paint. 

He said there is a high chance I'll have to continually clear the lines because tree roots will constantly grow into it, and because the line is made from old clay tile.

Tonsssss....subway tile takes time and don’t let your grout dry or you are screwed!

Tile search yet?

The interior looks decent with only cosmetic rehab needed, some appliances changed, new floors, and a re-tiling of a couple of bathrooms.

On my first 2 houses, I bought the cheapest square ceramic tile that looked decent enough from Home Depot or Lowe's.

Find a pattern for what works and copy them.

Replaced all carpet and ceiling tiles.