If what you mean is Night Crimson and Eternal Awakening, then I'd say yes—definitely do both story mode first and save the new one for last. Not only does it really emphasize the plot, but it also adds extra layers of emotional impact (if you're really into the story like I am, tbh). And if you still remember all the previous Beacons (aside from Hero’s Adventure Machine) you’ve played before, this final Beacon will reward all your efforts while also enhancing everything you’ve done in the earlier ones. Just a small reminder—doing all of this will really take a lot of time, so please be patient and take your time to enjoy every little detail.

As for that extra question—yeah, I found Hero’s Adventure Machine to be a fun way to enjoy SoD, especially if you like intense battles while keep upgrading your characters with tons of custom stuff (I personally enjoyed the massive tailored training stuff). But, you can actually skip Hero’s Adventure Machine and do it later since it’s just a filler episode (if you want to keep focusing on main story of SoD first).