D&D 5E Wizards values the power of conditions and noncombat effects as virtual damage.

[Steady Vane]

That did point me towards the answer! (Thanks!) In this case, I don't think it's taking into account the petrifying effect at all.

The Medusa's hp and AC give it a defensive CR of 4. There is no debate there, thats how it works. The attack routine also gives it an offensive CR of 4. So, if we ignore the special ability, it's just a CR 4 creature.

So, what if, instead of messing with the petrification, they are assuming all the PCs are averting their gaze to avoid getting petrified? In that case, the PCs are effectively blinded against the medusa the entire fight. That means they have disadvantage on their attacks and it has advantage on attacks against them. And in monster design, that converts to a +4 effective AC and a +4 effective bonus to attack. Since each +2 raises the CR of its respective part (offense or defense) by 1, that means that both offensive and defensive CRs (and thus CR in general) increase by 2. Which bring that CR 4 to the listed 6. Either that or they are just treating it as 21 damage for action denial and didn't count it twice for multiple targets (One would think they might have caught their error for the 2024 version if the latter were the case though.)

As far as your direct points, I think you are probably right that they are going with single target damage from a spell converted to the condition. If that is what they are doing though, it means they are not valuing condition causing spells as much as damage causing spells, because otherwise they would be doing it the way I described before (which is how they do actual damage and damage spells). That in and of itself is a noteworthy concept.

I'm also leaning more strongly into the idea that they really are only treating the strongest condition as 2nd level action denial. I mean, what conditions (other than dead) actually have a stronger impact on the battle than taking a character out of the fight for a round? The only one I can think of is getting PCs to attack their allies. That would likely count as a 4th-level effect, and it's anyone's guess what virtual damage they would assign to it.

And I'm wondering now about the cantrip and 1st level values of 5 and 11 offered in the OP. If we are taking magic missile and rounding it up from 10.5 to 11, why are we going with 5 for a cantrip? I would assume fire bolt rounded up from 5.5 to 6. Or maybe those values are derived from the DMG tables. But, as Jeremy said, thats not actually where the condition-equivalent numbers are coming from. Those come from the strong iconic damage spells. Otherwise 2nd level would be 16.5 from the table, rather than the 21 from scorching ray that it is.

And it seems from that that chromatic orb might be a better one to pick for first level, giving us a virtual damage value of 13.5, rather than 11. Anyone's guess which way to round. In general, design tends to round off, as opposed to the in-play rule of rounding down.

Probably late to the game here, or I would have been asking the OP about his numbers when this thread started.

Hey so I was using the average real values by CR from Blog of Holding and Forge of Foes. That was the data points lol, the DMG guidelines are kind of skewed from what monsters turned out to be. You can technically get to the printed monster stats by following the DMG guidelines but it takes a lot of fiddling, so the table is not the true averages by CR.

As for getting damage from spell comparisons, there's a bit of art and a bit of science to it. The easiest is when a spell has a clear cutout for the effect's damage, like in Tasha's Mind Whip. Past that it gets funky quick. Mostly because while there are clearly laid out rules for damage spells, the criteria for where a purely non-damaging spell may end up seems a little arbitrary and can account for other spell factors. For example, power word: stun auto-applies under certain conditions. That would affect its "psuedo" damage; but it remains unclear how it would do so precisely. Or Thunderwave, level 1 spells do slightly too much damage, but if valued as a single-target spell as if used by a caster to knock away melee enemies, then the push effect would be "worth" 1d4 damage. But as an AoE, would that be only 1 damage per target? Is that even the correct value to be aiming for? Like I said, it gets funky quick if the spell is not super straightforward with the same exact use case. Namely single target, no effect on save.

Part of this is also some spells, such as the aforementioned power word stun, got changed in 5.24, and we can compare discrepancies. WOTC seemed to think Power Word: Stun did too little in the base 5e version, and made it have a negative on a "save". So even comparing spells, clearly some spells are valued more correctly than others. Or maybe not.

Since this mechanism exists I don't know why this guidance wasn't published in the DMG 'making a spell' section. It'd be much easier than all this guesswork

 

[Steady Vane]

As for not valuing the conditions properly using this system, short answer yes. You are totally right, the quirks lead to undervalued status effects in general it sure looks like

 

[delericho]

Since this mechanism exists I don't know why this guidance wasn't published in the DMG 'making a spell' section. It'd be much easier than all this guesswork

"The secret we should never let the gamemasters know is that they don't need any rules" - Gary Gygax