At my lab, those values for c3 and c4 are in the normal range... are you sure they are out of the normal range for your lab? c3 value is very much textbook/in the middle normal and the c4 is low normal but you'd need to be .15 or lower to be out of the normal range.
MCTD has quite a varied prognosis much like lupus. If scleroderma is the primary disease process, then prognosis for that could be worse than for someone with "mild" lupus. But overall, it is probably very similar to lupus or possibly better.
Knowing that you are RNP positive may help explain why they wanted the lung function test done, to try to determine if anything is going on with your lungs and to try to rule out MCTD (with a scleroderma component) or get a baseline value on your lung functioning for future reference.
Right now though, it seems pretty unlikely that you have any sort of scleroderma component as you have not complained of any symptoms that are specific to scleroderma. So don't worry about it.