Remember also that penning for breeding doesn' take all that long. If the rooster is a bachelor and the hens are kept separate during the fall moulting season, when they want zero attention from a male suitor nor laying anyway, they come out of moult in January, let us say. In January, one might be feeding them well, helping them regain the form and feathering. Then, in February, the days are now long and finally, the hens are laying again.
After four or five days in the breeding pen, she'll likely laying fertile eggs, the very eggs, from the precise matchup you desire. Let's say you have 4 breeding hutches set up. Each with the trio from your example. If the hens are laying 5 eggs per week each and you have 8 hens in 4 breeding pens or hutches, you'll easily fill your incubator in a week. You might then leave you pens together, or you might use the 3 week incubation time to do some re-arranging of mating pairs/trios.
After you hatched two or three incubators of live chicks? It is likely April and you're about done hatching for season. You can then break up those breeding pens.
The point is simply this. You're not keeping your small breeding pairings together for all that long. Hope that helps.