How can I specify LowRes or HiRes for specific output transforms?

You can control this via the Output Generator conductor files. For example:

<target name="dita2pdfwrapper" depends="default_dependencies, flatten, resolve_container_keyref, extract_HiRes_images"> 

<target name="dita2xhtmlwrapper" depends="default_dependencies, flatten, resolve_container_keyref, extract_LowRes_images">

For the target named dita2pdfwraper, notice the dependency extractHiRes Images which means HiRes image type is preferred. If not found, the processing will take the default format. If this happens, your log file will include a message like Image type [hires] not found. Using default instead. The inverse is the case for the "dita2xhtmlwrapper" target.