happy to hear you have a new job.
I've been through redundancy due to company closure 3 times myself, but couldn't be happier where I've ended up, so hope it works out as well for you.
Since version 8.5 its been really rare that I've processed production jobs using Quark, I have kept my hand in testing Forum stuff at home.
So speaking generally with very little actual hands-on experience... but sound technical grounding...
v2016 if I remember has/had a nasty gotcha where if you select downsampling in your pdf Export settings bitmaps get sampled to Colour Image levels and look fairly terrible.
Each version since v9 has IMO handled placed pdfs better than the previous, though some thought 9 the best I think 2018 is the best so far. Forum posters have found different failures with each version, some that worked fine with earlier versions fail with later versions.
At some point placing EPS has become worse and less reliable, DCS>PDF>EPS>QXP>PDF isn't going to always work, I think there are scenarios where EPS gets treated like a pdf by quark so gets converted rather than passed straight through.
Output/Export 9 10 QX2015 QX2016 QX2017 QX2018 QX2018 Pro
Direct PDF export (without distiller) Yes Yes Yes Yes Yes Yes Yes
PDF Export using technology by callas & Adobe No No No No No Yes Yes
Export tagged PDF No No No No No Yes Yes
PDF/A export No No No No No Yes Yes
Pass-Through Transparency No Yes Yes Yes Yes Yes Yes
PDF/X-1a and PDF/X-3 Export Yes Yes Yes Yes Yes Yes Yes
Direct PDF/X-4 Export No No Yes Yes Yes Yes Yes
Export layers in PDFs Yes Yes Yes Yes Yes Yes Yes
PDF Export using technology by callas & Adobe is quite a biggy . As I understand it, Callas help with the code for Acrobat Pro's Preflight and Fixups so their technology inside Quark can only help it get placed PDFs more correct. This is also going help with placed ai files.
Pass-Through Transparency : Not sure what this means, I sort of thought it meant placing a pdf that contained transparency would retain that transparency upon Export, but I'm not seeing that in my tests?
Direct PDF/X-4 Export : to me the implication here is icc profiles can be passed through to pdf... yay
, sadly no
, its possible to pass PDF/X-4 criteria without.
Converting PDFs (or ai objects or even idml or InDesign objects) to quark Native objects, is all possible in 2018 and its improved from 2016. 2017 and 2018 let you save out the individual images too. Its pretty cool stuff but you have to remember you are CONVERTING and not be worried about the inevitable subtle changes (for me I'd try Pitstop then Illustrator then Quark or Affinity in that order, and having to make some serious edits and justify the time involved ... but its always good to have options)
There is a lot of HTML5 and ebooks and app stuff that I haven't looked at in the later versions, probably a lot of cool stuff but of no interest to Luddites like me.