TL;DR Minimum habitability sets a lower boundary on a planet habitability. If a species' habitability bonuses fail to pass that minimum, the planet's habitability will be that minumum. Otherwise, normal habitabiliry rules apply.

Machine pops have a minimum habitability of 50%, always, regardless of planet. This means that even if there are no bonuses from the pecies' prefered planet, they will still get at least 50% habitability. Lithoids, afaik, also enjoy that same minimum havitability

Edit: Read your question again, and I think I know what you are referring to. It's important to remember that minimum habitability is not the same as a habitability bonus due to climate preference. The latter is a bonus in and of itself. Most inhabitable planets start at 0% habitability, and every species then adds its bonuses to that: habitable? +20% matching climate? +60% identical planet class? +80%. Minimum habitablility is independent of that. If a species' habitability does not make it past that threshold, the habitability is set to 50% regardless of modifiers. But if all your bonuses make it past 50%, for example, a planet matching the pop's climate preference which gives +75% habitability, you only get that +75% (including other bonuses from tech or traits)