Definite support for pebble based boxes as we need more pebble sinks unquestionably, that said, while I do feel like any box would need to have a mildly substantial pool to really incentivize interest, putting everything in hypothetical pebble boxes would probably devalue the existing companions pretty substantially from an economic standpoint and have an adverse effect on the value of moonstone companions as opposed to helping the pebble economy. Even if made rare, the Moonstone companions would very quickly become much cheaper to buy with pebbles than how they're valued at moonstones currently. This would upset people who previously purchased the moonstone companions and make it so something entirely pointless to buy with moonstones exists within the shop to tempt people who don't know it's 10% of that price on the flea market. No opinion whatsoever on the referral reward companions, as how they exist right now has no impact on the economy aside from people buying referrals to get them, which is a user made market.
Blind boxes on websites like Gaiaonline where they add old items to their pools (without recoloring them or anything) always severely devalue all the old items added. When a user buys tons of boxes and opens them intending to find a unique prize, old stuff and common items pile up and get resold at cheaper and cheaper prices.
Here's an example, the Dustravens right now, on the marketplace, are 4.4k pebbles. Lets say the Onyx Dustraven is one of the "common" prizes in the 90k pebble box. Even though it cost 90k to get the raven, people are going to want to liquidate that pet to get some of their pebbles back, because the raven doesn't really hold much value. If say, even 10 people buy the pebble box and want to liquidate their ravens, you're going to see all 10 of those people undercutting each other on the marketplace. But in practice, it would probably be a lot more than 10. We would very likely see them selling for exactly 1 pebble over their sell to vendor price almost instantly.
In general, no "common" item from a box is ever going to be worth more than the box itself, without a massive pool, but with the pebble prices for familiars being largely just a quarter of the proposed price to begin with, they would all be severely devalued on the Flea Market across the board by this, and in some cases simply be worth less than nothing. Essentially it's a recipe for companion inflation, and it would make using the mole shop to buy them pointless.
So I would support pebble based random boxes, but not if they included non-recolored, existing companions. There is 0 economic benefit to making existing shop companions cheaper. It's also unfair to anyone who bought a moonstone companion or an expensive pebble companion in the past.