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zeroing the bushings has always been a part of the honda service manual instructions. (nobody seemed to pay any attention to it until i mentioned it...) you didnt post a scan of the HFP instructions but i imagine it looks very similar to the service manual.
it is assumed you are only replacing the shock/spring with the same shock/spring so ride height doesnt change. in the process of removing the shock, you only really have to loosen the shock bolt, and the rear outer lca. the front lca has the ball joint at the end. so those are the only bushings you really need to retighten under load so the bushing is not stressed and overly rotated and eventually tear, leading to shitty suspension. not the bushings fault, just poor installation.
now when changing ride heights or swapping lowering springs, it would be best to reclock ALL the bushings (some you cant, easily at least), but for a small difference of ride height, its really not a big deal. sure, its better if you did reclock other bolts you can easily access. but rubber bushings do have a wide range of normal operation. the point is to avoid locking the bushing in a sagging position and expecting it to operate level in normal conditions, thats too much.
This isn't even a Honda thing, this is a rubber bushing thing. Tightening the bolts while the suspension is in full droop leads to stiction when the suspension compresses. This is even more evident with stiffer bushings than stock.
If you feel better loosening and then tightening the rest of the bushings, it won't hurt anything. I always do.
When I went to get an alignment , I did instruct the shop to re set all the bushings before aligning, but doubtful about the extent they did.
I'm thinking of going to another alignment shop just to ensure they reclock the bushings on the rack (ill hang around and watch this time), for peace of mind.
I'm hoping if some are loaded and then re set, this won't radically alter the height to the point I need another alignment.