Treat the Dragon's CR as 20

In the specific example you give at face value the current CR seems appropriate, but I would argue given how the spell works and its effects that it was specifically designed to deter low level players and weaker creatures from entering. While the shape-changed dragon has some of the stats of a lower CR creature, it retains some of its own stats, abilities, and actions. Ultimately its a question of whether you believe the magic in D&D is essentially aware of the narrative, a CR20 dragon is an incredibly powerful entity even if temporarily within a "weak" body.

On a DM meta level just always treat the CR of a creature as its true-form, the mathematical threat to the party that CR representsif a fight occurs is still the same.

Their calculated CR remains the same, but they are far stronger

Carcer rightly points out the way your CR is calculated, but I feel like that doesn't capture the entire picture.

I feel like this pseudodragon may very well be punching above its 1/4 weight with a 2d6 breath weapon. With a lucky roll, there's a good chance it could knock out an entire first level party in a single breath weapon. CR 1/4 indicates it should be roughly 2-3 pseudodragons to form a decent challenge for a first level party, but 2-3 pseudodragons with this breath weapon will absolutely annihilate any first level party round one if they know how to aim.

Ogres suffer from a similar problem. If you calculate their CR, it comes down to a CR 1 creature, but they are still listed as a CR 2 creature, simply because there's a really good chance that it'll oneshot a first level character.

On top of that, you've replaced their attack which requires getting in melee range with a breath attack they can use from a distance. This, combined with a fly speed of 60, means they can very easily fly into range, breath weapon, fly away, and then fly away until their breath weapon has recovered, before coming again for a new run.

This is at a level where most characters will have very few ways of dealing with a flying opponent.

I for one would not want to face even one of these creatures at level 1.

If the breath weapon is changed to be once per short rest instead of Recharge 6, it'll at least make it a lot more manageable because it can't hit and run. Also reducing the damage to 1d6 may very well be enough to keep it around roughly the same challenge rating. It'll at least no longer be something I'd really dread fighting at level 1.

As an aside, regarding being used as a familiar (say, for a Warlock via Pact of the Chain), it's most likely not that big a deal, I doubt it'll be more impressive than invisible scouts. Familiars used for combat purposes tend to be dead familiars before long. It'll be good for killing some goblins every now and then, but it'll be costly to keep resummoning your dead familiar.