New answers tagged transparency
You asked that ages ago but, maybe useful for some, as not answered yet... You said that you are keep your adnotation in the map but if you save them in a database You will have full control over the adnotation, including transparency is it something you have been looking for??
You will find the annotation layer in the properties of your dataframe. I do not know (yet) how to make them transparent.
In QGIS you can organise the layers so that points are on top in the layers pane and just set their style differently. See image:
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