David,
Re my previous post, your question also implies a workflow that will go to Indesign, and well such a workflow is always a source of problem - I got good results nonethless even on transparency, and transparent gradients, with PDF export from Scribus, and import into InDesign. Nonetheless I was unable to check whether CMYK colours remained in the case of Scribus PDF imported in InDesign.
Direct PDF export from Inkscape was not so good with the loss of transparent items when imported in InDesign. Such PDF can be imported in Illustrator but not modified!
As a matter of fact, creating a gradient where the second colour ONLY has a transparency seems not supported by Illustrator (and very simple in Inkscape). Even creating a gradient fill with only ONE transparent colour in the gradient seems unsupported by InDesign (my latest investigations). Therefore if it was specifically what you intended to do, you may be trying to get InDesign to do what it does not support, even when designing objects from scratch. In the case of the Scribus PDF imported successfully, transparent gradients lead to blending with the background, which of course is not acceptable for a logo, but may still be what you want to achieve.
I hope you find this information useful.
Cedric
My advice is the following workaround : create your SVG, import it in Scribus, in Scribus, redefine your colours as CMYK and save as EPS (remove unused colours).