i think charlotte is the best of the bunch you offered in terms of matching, although charlotte is significantly more popular now than phoebe. phoebe is hard — it doesn’t have many obvious nicknames, it’s got a ‘ph’, and it’s just a bit unusual.
i think another name that ends in the ‘ee’ sound (riley, millie, bonnie) is hard to do, but i personally feel that rhyming names are a little tacky. if you don’t, i say go for it! and i think a name like riley (much as i like it) is too unisex for regal phoebe. same with addison. rhiannon is nice, because they both have an ancient feel, but the combo seems a bit clunky to me. sienna…there’s nothing wrong with it, it just happens to be a name i don’t care for. sorry!
i really like the name diana with phoebe — it’s one of my favorite sister sets of all time, actually. phoebus was another name of apollo, the greek sun god; diana was the roman equivalent of artemis, apollo’s twin sister. so it’s got a yin-yang thing going on that i really like.
you could also create a through-line between their names by using a same or similar meaning — lucy/lucia, clare/claire/clara, elena/eleanor/helen/helena all mean light or bright.
the other thought i had was using the greek connection. so many beautiful names that are familiar, but not hyper-popular, come from the greek myths or language. some favorites are: ariadne, calla, cassandra, daphne, damaris, evangeline, iris, junia, lydia, and maia/maya.
i think, of all these, my favorite pairs are:
phoebe and charlotte
phoebe and rhiannon
phoebe and clara
phoebe and eleanor
phoebe and diana
phoebe and ariadne (it’s got that ‘ee’ ending, but they’re both so cool!)
phoebe and lydia
phoebe and iris
hope this helped!