Hi AndrewG,

It would be helpful to post a .3dm file, at least of the area in question.

BlendCap script could be helpful, but needs one closed edge.
Starting with a rounded rectangle, Rebuild will create one closed curve, which can be extruded, without endcaps.
Delete the curve, and select the edge, run BlendCap. Combine with the bottle...? Maybe Boolean delete from solid bottle? May need a little fillet?
(I have not tried a curved rounded rectangle.)

- Brian