Two instances of skipping an untap step will indeed happen consecutively.
Comprehensive Rules wrote:
614.10. An effect that causes a player to skip an event, step, phase, or turn is a replacement effect.
“Skip {something}” is the same as “Instead of doing {something}, do nothing.” Once a step, phase,
or turn has started, it can no longer be skipped—any skip effects will wait until the next occurrence.
614.10a Anything scheduled for a skipped step, phase, or turn won’t happen. Anything scheduled
for the “next” occurrence of something waits for the first occurrence that isn’t skipped. If two
effects each cause a player to skip his or her next occurrence, that player must skip the next two;
one effect will be satisfied in skipping the first occurrence, while the other will remain until
another occurrence can be skipped.
614.10b Some effects cause a player to skip a step, phase, or turn, then take another action. That
action is considered to be the first thing that happens during the next step, phase, or turn to
actually occur.
Note: This is functionally different from casting two
Sleeps on a single opponent in the same turn.
Activating Scion and then reanimating the hard copy will only cause one of them to die, as the legend rule was updated in M14 such that a player chooses one legendary permanent to keep and puts the rest into their owners' graveyards as a state-based action. But yes, if you choose to keep the original and Scion was your commander, you would have to let it hit your graveyard in order to get the "dies" trigger. "Dies" is more or less shorthand for "is put into a graveyard from the battlefield," and is used exclusively when referring to creatures or things that are
expected to be creatures.
Comprehensive Rules wrote:
704.5k If a player controls two or more legendary permanents with the same name, that player
chooses one of them, and the rest are put into their owners’ graveyards. This is called the
“legend rule.”
700.4. The term dies means “is put into a graveyard from the battlefield.”