> ... "save to pdf" is not able, to generate one file with different pages sizes.
Reportedly, Print-to-PDF, and Print-to-ps&Distill can, if the PDF job options are set to the maximum page size.
Also search the forum for "PDF different page sizes".
Never having had a need to do it, and Adobe documentation for Acrobat being what it is, I can't tell if AcroPro is supposed to be able to merge bookmarks when merging PDFs. It would be an unsurprising feature, and you do say it works on PDFs generated by means other than FM.
Here's a hack that might work, if the variable-page-size rendering turns out to be out of reach. You can batch* this.
Open each component PDF and re-save it with some otherwise harmless optimization (or even none). This will probably cause AcroPro to re-write the internal structures of each PDF, which might then be amenable to merged bookmarks when you re-open them for merging.
* We do a similar thing for a slightly different problem. We have a software-in-a-box XML publishing app that, at just some seats, is generating PDFs that are tagged for byte serving (fast web view), but are not in fact encoded for it. This causes AcroReader plugin and entire browser crashes for web end users. The s/w vendor can't even tell us where the option is for controlling that feature, because they get the PDF gen code from some other 3rd party. So we routinely batch process all generated PDFs, with, oddly enough, NO "commands" selected. The re-save alone fixes it.
For the merging of pdf, bookmarks:
I've tried several methodes of save as in Acrobat, but nothing helped.
I've done already a lot of merging e.g. suppliers documentation. Since I've used Acrobat (Vers. 7), the bookmark always merged as well. Those bookmark usallly where linked with the page, not with a named destination. I'm going now to ask in the Acrobat Forum.