I would like as little delay between exposures as possible - while at the same time letting dither settle. The download for my Atik 383L+ takes many seconds - and if dither happened before the download it would allow the guider to use that time to settle. I am using MetaGuide but it seems like this would apply to other guide software also.
Basically anything that is disruptive to guiding should happen immediately when the exposure ends and before download begins. This includes changing the filter - especially when backlash compensation kicks in. Then the download time and other overhead can be put to good use - letting the guiding settle.