You can change the color of the comment (to white, for instance) and thus change the color of the bubble, though I don’t think there’s a way to pick a part of the gradation–you’d just have to select the color for your notes based on what you want the bubble color to be (the color you pick is the darkest end). White is white, though, and I find it easy to ignore when reading through a doc.
To change multiple comments, load all the documents in a Scrivenings session, show the comments in the inspector and select all, then right click on a comment to bring up the context menu and use “show colors” to assign your own. This will affect all comments but won’t change the footnotes, if you have any, so you can easily differentiate.
If all you’re doing is reading through, and not making new edits, you could also just make a clean copy of the documents (either copy/paste without comments or duplicate the documents and then strip the comments from them–or compile the whole thing and then read it outside of Scrivener or import the compiled file) or take a snapshot of the documents and then wipe the comments to create a clean version.