#2 She could get involved in the match at a later date
Let's assume for a minute that Charlotte Flair wins the Royal Rumble match. She challenges Ronda Rousey and the WrestleMania match is set in stone. Becky Lynch has two pay-per-views since then, to get herself involved in the said match.
The Royal Rumble pay-per-view will be followed by Elimination Chamber and Fastlane, as we head into WrestleMania 35 and beyond. This means that Becky Lynch has two opportunities to become part of the huge title match. This is not counting all the SmackDown Live episodes that she'll be part of.
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Not having Becky Lynch in the Royal Rumble match is hardly the final nail in the coffin for 'The Man'. In fact, it opens up a new chapter in her story and could certainly be better for her, over the long her.