You need to realize that you can't directly compare installed per sq.ft. costs for 350 square feet to 1000 sq ft or more. Sure material costs and installation effort are proportional but there are minimum set up, procurement, disposal, etc. costs that start ata fixed number. Unless the underside of the roof deck is visible, you won't be able to assess its condition without tearing off the old.

A single-ply membrane either rubber or plastic would be my choice over roll or built-up.

good luck

If the roof is EPDM membrane, it wil be a single layer.
The ony issue with EPDM for retrofit is that it is damaged by contact with asphalt.
If there is an existing asphalt roof it needs to be removed down to bare wood, and even then a layer of fresh wood is better than taking a chace on damage from asphalt on the deck.
If the proposed roof is bitumin (AKA 'torch down') it is not really rubber and can be applied over any flat smooth surface. Either bare wood (even if it had asphlat) or a fresh layer for integrity.
Neither of these materials are very good at spanning any kind of gaps, so surface preparation is iportant. They can cover the normal small expansion gaps of plywood decking.
EPDM is the better of the two, with lifetimes in excess of 30 years.

I'd opt for EPDM, and as brickeye wrote, tear off the existing.

Add a new layer of half-inch or 3/8ths-inch ply (if going over old existing sheathing) or 3/4" ply if going over the framing, and put the EPDM down over the new ply.

Mongo