Toronto Loses Replay Review Due to Lack of Appeal After Boston Batter Alex Verdugo Misses First Base

Replay Review confirmed 1B Umpire Doug Eddings' on-field ruling that Red Sox batter-runner Alex Verdugo was safe at first base in Toronto despite the runner missing the base his first time by. Was this the correct call? Article: www.closecalls...
The video indicates that as Blue Jays first baseman Lourdes Gurriel stretched to field a throw from middle infielder Marcus Semien, he not only broke contact with first base before catching the ball, but batter-runner Verdugo also missed his touch of first base by leaping over the sprawled Gurriel.
Essentially, neither player touched first base that "first time by."
After the initial action, Gurriel spun around to keep an eye on Red Sox baserunner R2 Bobby Dalbec, inadvertently placing his foot on first base with the ball on his glove..... so how was Verdugo not out for missing a base?
The answer can be split into three parts.
First, the "real-time" play at first base itself. Official Baseball Rule 5.05(b)(3) Comment states, "If the batter-runner misses first base, or a runner misses their next base, they shall be considered as having reached the base." Thus, Verdugo was considered to have reached the base as soon as he past it, whether or not he actually touched it. Because Verdugo passed first base before it was tagged, he is considered SAFE for the purposes of out/safe timing (e.g., "force play" timing).
You'll notice we talked about "for the purposes of out/safe TIMING"-so the next rule talks about the purposes of out/safe TAGGING. OBR 5.09(c)(2) governs missed bases: "Any runner shall be called out, on appeal, when-With the ball in play, while advancing or returning to a base, they fail to touch each base in order before they, or a missed base, are tagged." Although Gurriel placed his foot on first base, he failed to specifically appeal that Verdugo missed first base. Without a valid appeal very clearly specifying the infraction-to-be-appealed, the umpire by rule shall NOT declare the runner out. An umpire can't "assume" an appeal nor credit a team with an appeal if said team has not clearly conveyed their intent to appeal.
Finally, we see that Verdugo after overrunning first base returned to first base and stood on top of it (e.g., touched it). This is known in the MLB Umpire Manual as "last time by" and Verdugo's action in returning to and touching first base his "last time by" is said to correct any previous baserunning infractions that may have been committed at that same base. in this case, "last time by" cures Verdugo's initial missed base and effectively closes the window on Toronto's opportunity to appeal (not that the Blue Jays ever actually appealed anyway).
Thus Charlie Montoyo's challenge properly resulted in the original safe call being CONFIRMED even though the runner failed to touch the base his first time by....because the runner DID pass first base before the fielder's tag of the base, Toronto failed to appeal the runner's failure to touch the base, and the runner cured his earlier infraction by returning to touch first base his "last time by."