Ok, lets start with the first questions
I use Roche systems, and in fact I can change the threshold values after the PCR is performed, calculate the most important statistics (like mean values, standard deviations, standard error), so I guess I won't be able to help you with your software unless I see it.
The fact is you can't compare two different experiments, even with exactly the same PCR efficiency, having two different threshold levels, cause it affects Cts.
And the second question - yes, usually, yes
Seldom, but for some types of samples I have problem with efficiency. In most reactions I get more than 90%, reaching 96% for PCR (not RT-PCR - for that I sometimes get higher values). But for some reactions I constantly get 88-89% and I can't do a lot about it and I don't. This is because for my samples, in which I have some inhibitors, I just have PCR efficiency constantly on the same 88-89% level and I leave it like that. This is just the most relevant to environmental sampes I analyse. I can't improve it on the cost of DNA purification efficiency and I don't care about the amount of the final product. As long as the efficiency is known to me, and it is close to 90%, everything is fine.
Off course there is a problem if your efficiency falls - that reaction conditions are not relevant for exact quantification.