On behalf of Adobe, to summarize and expand on the thoughts presented here:
(1) Any PDF produced via creation of PostScript and distillation to PDF is by definition going to lose live transparency and any color management. The PostScript imaging model doesn't support transparency. There are no plans to update PostScript further (that is what PDF is for). Anything that is apparently transparent in a source document is flattened into opaque objects. There is no workaround for this.
(2) Professional quality PDF from publishing products really requires direct production of PDF such that attributes such as transparency, color management, tagging, links, etc. are not lost. This is why for Adobe's authoring / design tools, we strongly encourage PDF export / save and discourage Luddite workflows that involve PostScript
(3) Adobe has no control over the PDF that Microsoft produces. Complain directly to Microsoft.
(4) Quite frankly, Publisher is almost universally reviled amongst print professionals given the “issues” it has. Those who love it tend to be corporate bean counters. 
- Dov