since the text in my random sample(Vylon Material) said "If... You Can..." that card will not missing the timing, only a "When...You Can..." optional effect will missing the timing.
If you synchro summon, card like "vylon material" will start a chain in the response-window for the synchro monster.
So the equip spell card will go to chainlink 1 because it's triggered earlier, even if the synchro monster have a mandatory trigger effect(i.e: Mist Wurm), it'll go to chainlink 2, after that your opponent/yourself may respond with card like Torential tribute or something.
However In OCG, the mandatory trigger effect will be placed in chainlink 1, while the equip-spell-card will be chainlink 2 though...it seems you'll follow the OCG rule since it's still an OCG card
If I'm not mistaken, Equip-Spell-Card is just sent to grave if the equiped monster is no longer a valid target, so that wouldn't trigger vylon element's effect...I'll look around bout this later.
if you mean, for watever reason the equip spell card is destroyed(as the last thing to happens(No Ryko,not being destroyed in chainlink 2 while chainlink 1's activation isn't negated etc.)), then" Vylon Element" and Vylon Equip-Spell-Card will form a chain, with you allowed to determine the order(Just the common SEGOC.),
And please note that activating something never mess with timing, It's like saying Bottomless will miss the timing against caius because the last thing to happen even is Caius activating his effect.