About the first issue, you are right: FlexCel considers that you want to print what is in the print area. If it is outside it won't print it, so if print titles are outside the print area they will be ignored. I will be honest, this makes more sense to me than printing the print titles anyway even if they are not in the print area, but as Excel indeed behaves differently we will see if we can adapt the code to behave the same.
Note also that you can use multiple print ranges in a sheet and FlexCel fully supports that. So you could add the print titles as a separate print range, even if that wouldn't be the same as those print titles would be printed in a separate page too.
About the second issue I couldn't reproduce it. I tried with the following file instead:
http://www.tmssoftware.biz/flexcel/samples/printtitles2.zip
And it works correctly.
There is though one known issue when printing tagged pdfs (the default) and print titles which hasn't been fixed yet. It doesn't happen in most cases, but it can for complex files. So I wonder if you set:
pdf.TagMode := TTagMode.None;
(and you also add FlexCel.Pdf to the uses list so it compiles)
Does it make any difference?