Playing MR3 again, I have a few breeds that are not available to me on CDs at this time (once I buy some blanks I can fix that, at least).

The thing is, since I was missing them on disks, I decided to try to get the encyclopedia entries from the in-game saucer stones that can be gathered on ventures. This wen pretty well for some breeds, but I have yet to see even a single saucer stone piece for the following breeds:

Pancho
Joker
Dragon
Beaklon

and the ones I have on CD but can't find stones for in-game:
Raiden
Zan
Ogyo
Durahan

Am I just having a run of poor luck, or are some of these monsters actually not available without a disk to regenerate them from?

the FAQ here for this game seems to imply that all main breeds are available from the in-game stones, is that the case?

Note that I have never had these available without (real-life) disks - I have had about 3 previous files, spanning roughly 130years - or, approx. 200 RanRan adventures with the 2000G extract to fail to find these stones in, even going so far as to never see a rival offer one in trade, as far as my notes are concerned.

Have you tried trading chips with the visitors who come to your ranch to battle? They can have some good chips on them.

Yes, I was including the ones people brought to trade - so by that I suppose I've just gotten very unlucky to not see these monsters' chips? If that's the case I'll just have to be patient and wait out the bad luck I suppose.

My memory of old files isn't perfect, but I kept note of chips that rivals brought to trade and that I found on ventures, because I wanted to have a list of (main-breed)monsters available within the game itself and all these monsters are absent from that list as well as not showing up on my new playthrough.
I check the chips rivals offer for trade whenever they show up, just to see what they have, unless I have no chips of course (because Fleria won't let me check).

Dragon and Beaklon chips are available in-game. Because Dragons are available, because they are unlocked a similar way, I would assume that Durahans and Panchos are also available, though I've never found pieces for either. As for Zans and Jokers, I have no clue, but because in the game both breeds are near-unheard-of and considered dangerous and Tecmo has a decent eye for those things, they likely aren't available in the game. As for Ogyo and Raiden, I've never found their chips, but it seems sensible to me that they exist but are rare since tey are so scarcely found on CDs (in my experience).