[Stiglr]

Cap option for extrude works fine for me, as does the option to reverse the side the extruded surfaces face. Perhaps review your choices for 1- or 2-sided objects, and/or try to select the "invisible" capped surface and see if maybe it IS there after all?

After a quick experiment, I found that the "Remove original" check box in the Extrude feature set doesn't seem to be working properly. I created a sphere, selected one surface and extruded it with Cap End checked, and also with it UN-checked. I got the desired results both times. But, when I checked Remove original and extruded, the original surface was still at the base of the extruded stalk. (I had to remove the cap of the extruded stalk to check, but still, it was there, where a hole should've.

Vertex > Snap Together: this works perfectly. Select any number of vertices >1. Select the Snap Together menu item and they merge together (I think to an averaged location; I would prefer there be a way to assign which vertex location they all snap to, such as the first or last vertex selected!) However this does NOT merge all the vertices into one vertice. for that you must immediately select Vertex > Weld Vertices. THEN all the snapped surfaces will be one single vertice, and any open edges (red or blue) will be filled in. After that, you can split a vertice and turn it into multiple ones (one for each surface which leads to another contiguous vertice in the object.

About sealing a hole in the center. You may not want to actually snap vertices, as this creates a point (bunching the hole), and you may want to actually cap a hole. To do this, in vertex select mode, select all the vertices, in order, around the hole in counterclockwise order. Then select Ctrl+Shift+S or Vertex > Create Ordered Surface. That will create a surface that caps the hole. You may or may not need to triangulate the surface, if Second Life requires triangulated or 4-sided surfaces ONLY.

I don't know anything about Second Life, so I can't help you with anything specific to that.