Both flaxseed and BOSS are fed for their high fat content, but the omega-3 to omega-6 balance of that fat is very different between the two.
Flaxseed has a higher ratio of omega-3 to omega-6, which is the reason why many people feed it. It can help to make up for the omega-3 the horse is lacking when it doesn't have access to fresh forage (the omega-3 content of grass degrades very rapidly after it is cut and dried)
BOSS has a high content of omega-6 and almost no omega-3. Whereas flaxseed is often fed to supply omega-3, BOSS is usually just fed to give the horse a little extra fat content to add 'shine' to the horse's coat.
As to the debate about feeding flax whole or ground, you'll find some very strong opinions on this (some that even insist it must be boiled to get rid of the trace cyanide content). I fed it whole for several years. Never had noticeable seeds coming out whole in the manure, and my horse always has a soft and shiny coat (well, shiny when it's not muddy...) Perhaps it's not as well utilized as fresh ground flaxseed, but I do believe it's still being mostly utilized. At one point I tried stabilized ground flaxseeds (Omega Max) but my horse didn't find it very palatable and it was much more expensive than the whole seeds.
I do believe that if you're going to feed it ground, it needs to be either a commercially stabilized product or ground fresh just before being fed; those omega fatty acids deteriorate rapidly once exposed to oxygen and will also go rancid. You can extend the shelf life for a few days if you have a refrigerator or freezer to store it in after grinding.
“The horse is a mirror to your soul. Sometimes you might not like what you see. Sometimes you will.” - Buck Brannaman
"Nothing forced can ever be beautiful." - Xenophon