Comment 2 for bug 1028425

Unfortunately, the committed change (linking the 'Alpha' slider to the global opacity slider for the special case of selected gradient stops) does not offer a solution for related
Bug #169019 "no way to change fill/stroke opacity with gradient / pattern":
<https://bugs.launchpad.net/inkscape/+bug/169019>

Underlying issue of bug #169019 (AFAIU): The existing style attribute of an object with a gradient may or may not include a 'fill-opacity' and/or 'stroke-opacity' property (represented in Inkscape with the 'Alpha' slider in the color chooser for flat fill and stroke colors).
Inkscape itself is inconsistent whether to keep (gradient tool) or remove (fill & stroke) existing 'fill-/stroke-opacity' properties from a style when converting a flat color to a gradient (or pattern) paint server. I don't know about SVG files created externally, but AFAIU the SVG 1.1 specification does not prohibit a 'fill-/stroke-opacity' setting in combination with paint servers like gradients or patterns.

See also:
«When you have one of the gradient handles selected, its style (color and opacity) is reflected by the selected style indicator (left of the statusbar) and the Fill&Stroke dialog. Previously, opacity of a gradient handle was reflected as fill-opacity and stroke-opacity; now it is reflected as master opacity (the "O:" spinbutton in the selected style indicator, the "Master opacity" slider in Fill&Stroke). This makes it much easier to view and change opacity of gradient handles using only the selected style indicator in the statusbar. »
<http://wiki.inkscape.org/wiki/index.php/Release_notes/0.46#Style_of_gradient_stops>