The drain should be part of the "sealed" drain plumbing, so it'll be sealed from the ambient environment under the slab. You won't have radon coming up out of the drain if that's what you're asking. Pricklypear pretty much nailed it regarding radon mitigation. It typically involves adding perforated pipe under the slab and bringing that pipe outside the house's envelope and up the side of the house to the roofline. A low CFM fan is added to the pipe, it essentially creates a slight vacuum in the pipe under the slab, drawing and radon out and exhausting it to free air outside the house. If you're going to make the basement into living space that will regularly be used, definitely run more tests. Multiple if possible. Sort of like getting "three bids" to qualify a budget. Radon can change throughout the year. Seasonal, dry versus moist soil, etc. If you have time it's best to test throughout the seasons. Regardless, a long-term test would be more reliable than a short-term test. Long-term active testing (90 days for example) would be more accurate than a short-term (48-96 hour) passive test.

That drain looks deep enough to cement in a PVC stub and glue a PVC adjustable drain that can be set approx to tile height and dialed to final finish. Below is a link to a compound that works well with plastics and cast iron. This compound was designed for PVC to CI and CI to CI hubs. Found at most professional plumbing supply houses. Here is a link that might be useful: Hercules Plastic Seal

"Run Toliet drain straight into Pit underground." Sewage ejection systems are NOT sump pumps. The pumps are not the same, and the rules are not the same.

if you raised it 2-3 inches, would it still be steep enough for water to flow to it though? if so, then you just need to remove the drain and extend it. this may involve busting up the floor there, but that can easily be patched with concrete. you will have to build it up with concrete anyway, self leveling won't work because then you end up with no slope to teh drain.