Oh, I forgot. TIGERSHARKS!

Anyway. Are you saying a Custodian is like a GC or BS in roll, I'm not sure. Assuming speed increases for the Emissary and Protector, the Protector would be a more nimble vessel than the Custodian, with a 25% higher top speed and needing to travel only 66% as far before executing a turn.
If that still doesn't set well with you, the only other thing I can offer is that the Custodian is the pinnacle of Tau design, currently, and may have more loving care in its workings than the Protector.
Just holding a measuring tape between the bases, looks like there is about 13cm of breathing room possible between bases of a protector and custodian when stems are at 20cm. I don't think the Custodian should just sweep the battlefield with tracking benefits, but it still seems a bit tight, as in purist fleets it will be the only thing offering the TS support the fleet seems to depend on.
Maybe 20cm with a 30cm option at cost?
I understand your argument for the aesthetic side of dropping the variant. On the other hand, I do want versatility in my fleet, even if it means kitbashing. One cruiser gets boring after awhile, if we want a long term enjoyable fleet.
Thats why I'm in favor of just offering balanced variants, and leaving it ultimately up to the individual how to represent it. He always has the choice afterall not to do so, and stick to normal Protectors. A Custodian variant would be cool too.
I was thinking a more dedicated gunship, or a more support style vessel. But thats just fun-time wishlisting.
I do understand the viorla in concept. 45cm is the 'gold' point of the Protector. I just think the penalties are too harsh to warrant it, as you essentially don't gain much if tracking systems are around, at the loss of great 30cm firepower and broadside lances.
I can see the Emissary being a 30cm ship, at least from the picture angle, the engines look darn big on such a small ship.
Made for getting water and ethereal caste members places, or escaping in a hurry with precious cargo, at the expense of great frailty in a cruiser, but enough integrity to usually take a volley that would blow an escort.
Harmonizes with the slower escorts as well, castellans being gunboat support and wardens being towed in close fleet support.