Size drives most of the other differences.
Bigger drivers need a bigger cabinet
The Arena 3's 4-inch drivers are physically larger than what fits in the Pebble Pro's compact spherical shells, which is the whole reason the Arena 3 sits on a bigger stand and takes up more desk space. That size also gives it room for dedicated on-speaker controls instead of a single dial.
The Pebble Pro's power scaling is the tradeoff for its size
To stay small, the Pebble Pro ships with a lower base power output and reserves its higher power tier for buyers who add a separate 30W USB-PD adapter. The Arena 3 doesn't need that workaround because its cabinet already has room for a fuller amp.
Optical input matters only if your source needs it
The Arena 3's optical support is a real edge for setups with a source device that only outputs digital optical audio. If everything you connect uses USB-C, 3.5mm, or Bluetooth already, this difference won't matter, and the rest of your desk setup, covered in the OSRS setup hub, is a better place to spend the saved space.