In chapter 3 is suggested to use Munchdew with bonsai, I've set 2 of them with hopping bonsai pot on top of them. Bonsai shows as working I see tree growing in it.
I always had to place leaves manually, too me the bonsai didn't seem to work, before any crafting altar was empty all area is chunkloaded.

In chapter 4 is suggested to use Kekimurus together with a Collector Crystal, but the Floating/Collector crystal is craftable only in chapter 5 because you need resonating gem that requires infusing altar that is available in Chapter 5.
Was the intention to use the one inside temples till you reach chapter 5?

In chapter 5 I'm using Rose Arcana and that is working great for me, I can see xp draining and altar filling because recipe becomes available in few seconds.

You can use a block placer (the cyclic one is recommended) to place leaves for munchdews.

Although the Kekimurus is unlocked at Chapter 4, the collector crystal is only unlocked at Chapter 5, meaning that, as you said, the option of using pumpkins with collector crystals is only available in Chapter 5 unless you use the crystals inside temples.

I'd recommend eventually switching to the Entropynnium/Shulk-me-not/Blacker Lotuses as those are the strongest mana generation methods available, although the Rosa Arcana is pretty decent if you don't want to use Munchdews.