About four years ago I purchased an engine that included a pair of 1.8 heads that were not usable for my purposes (SCCA F Prod). The heads have 48mm intake and I think 39mm ex valves in them. There doesn't appear to be any porting, polishing, flycutting or machining done on them except for the larger valve size and for using dual springs.

My question is what are the uses for these heads? I've seen the 48mm valve heads offered as a machining service by FAT. Are these a common set up for drag racing? They came on a motor using old Venolia domed pistons but the valve head was too big to fit in the valve pocket and had damages the pistons where they touched. Are these heads used with flat tops? Anyone aware of any other set up that uses these type heads?

My 2.0 heads have 38mm & 48mm valves with flat topped pistons with no valve reliefs. I had to send the pistons out to have valve reliefs cut in them, it was only $60.00, so you could use those heads with flat topped pistons or even small domed pistons if you measure all of your clearances and get them cut to suit. I would port and polish them.
Those bigger valves won't do too much good without any room to breathe.
As you probably already know, the 1.8 heads have an inferior spark plug location and I believe less room to enlarge the ports but they will still work, they're just not optimal.

I was going to suggest paper weight unless you were ready to spend a bunch of money to port them and make them not hit your pistons which involves cam profiles and rod length and modified pistons as mentioned above. and compression. Header to make use of the valve sizes and bore to use the valve size. Oh and carbs that will flow like a muther.

Oh man my head hurts.

I bought a car with a 2056cc with big heads like you mentioned. Guy could never get it running.
stock cam
stock exhaust
huge deck heigth like .120 or something

I just took it apart and sold the pistons and gave the heads away
and used the crank as a core. kept the stock flywheel (not sure why)

Check with Dan Hall of Dan Hall's Machine shop in Portland, OR. He was talking to me about a custom cam set up using the 1.8 heads on a 2.0 setup. He's done it before, and said it delivers good power reliably. This would be a carbed set up. I've been happy with all the work he's done on my 951, and will probably try this set up when I get more cash together.

FAT builds a 2 liter for off road racing crowd.. Class 10.. These 48x39or38mm heads work good on these engines.

Having spent a lot of time on the flow bench with every OE T4 head made by VW I can tell you that every one of them requires welding around the intake ports to make room for the extra port volume the 48mm valves need to flow effeciently. The castings max out at about 45mm. After that going up on the valve without welding doesn't help flow a bit.
A couple of years ago I flowed a non welded 48mm intake port prepped by a popular West coast guy that didn flow any better than our CNC 44mm port! Our welded 46mm port flows nearly 230CFM. Our 44mm CNC port flows 205CFM.
You could pull the seats and weld the seat pockets up and fit smaller seats. Other wise I would sell them.