Did GM make different versions of the lower intake manifold?

There can be changes in mid year or from year to year but not usually. I ran into a missing threaded hole when I installed an engine into my 1999 CHEVROLET VENTURE. What you will likely find is there will be a flat spot where the hole is supposed to be. Consider drilling a hole and tapping it so you can mount the sensor in the same spot. That assumes everything else is the same and fits properly.

I think where I would start is by visiting a local salvage yard and asking them if those parts interchange. My guess is the "99" is the year the part was made. It's pretty obvious my suggestion of drilling a hole for the sensor isn't going to work. Besides that, does that right passage in the center photo go somewhere or is that just an empty cavity? It appears to have no passage in the new part. That suggests it is not the same part with a few minor changes, rather, it is a totally redesigned part that bolts onto the same heads. The hole for the coolant temperature sensor might be in a different location but there could be other differences too.

I think my next concern would be that any design changes resulted in an improvement of emissions or they solved some running or performance problem, and the intake is just one member of a team of parts that work together. There might be corresponding changes to the heads, their cooling passages, even the computer controls. If someone at a salvage yard says the two parts aren't interchangeable, and they can't give you a specific reason, ask an engine mechanic at a GM dealership if they are aware of the differences. I mentioned my '89 engine in my '88 Grand Caravan. The only difference was the newer engine didn't have the port in the upper plenum for the ambient air temperature sensor. I just let the sensor lay on top of the engine and forgot about for the next 15 years!

It would seem to be obvious that the coolant temperature sensor is needed, but they might have relocated it in later years to make it more or less sensitive to small temperature variations. Also, if your sensor is a single-wire sensor, that will be for the gauge on the dash, not the Engine Computer. Perhaps newer vehicles didn't have temperature gauges so that port and sensor weren't used. The engineers have gone off the deep end with their insane need to computerize everything imaginable. Instead of two coolant temperature sensors, one for the computer and one for the gauge, they might be running the gauge through the Body Computer which gets its information from the Engine Computer. That would also eliminate the need for one sensor.