What Ryan replied is true for accessing a PDF annotation in code, but I believe you are asking how to programmatically trigger a visual selection of an annotation. Unfortunately there isn't currently a built-in mechanism to do this, so your choices would be to use the 'hacky' approach, or to modify the tools code to create a proper way of doing this. The latter will be nicer to use internally, but will make merging in new versions of the tools source code more time consuming. (It is best to subclass when possible.)
That said, having a standard programmatic way to visually select an annotation sounds like a good idea, so we'll try to add this to a future version.