Re: Strat PU, Cover on, cover off?
Hmm. What brand/model guitar? I have a APS-1 as well and it lines up well in either my Strat or my homemade Frankenstrat, although it's reverse angled in the homemade.
Check the string spacing of your guitar. Just measure from the middle of the low E saddled to the middle of the high E saddle. Then measure the HS3 and the APS-1. Same way, middle of low E pole to middle of high E pole. Post the measurements in millimeters. Also measure the string spacing where it is in the guitar, right over the pickup (high E to low E).