That's my point.I think you are looking at caster NPCs the wrong way.
Generally PC wizards are designed so that slots at wizard level x are balanced against other characters level X across eight encounters on average.
Monsters are balanced to be within a power window for their CR when facing a party in one encounter.
The typical wizard PC is actively going in expecting multiple fights in the day and spaces their slot expenditure out with that in mind. If they are expecting one fight per day or are facing being overwhelmed then the rational move is to nova instead. The default baseline though is multiple encounters within one adventuring day for PCs.
The typical monster/NPC wizard facing a party is either targeting just the party (expecting one fight) or being jumped by the party and seeing death coming in as they are overwhelmed in the fight. In either case novaing is a rational tactic for an NPC mage in the baseline expected encounter. Exceptions like an NPC mage fighting in one skirmish after another in an active war battlefront where they would need to pace out their slot resources are not the default NPC encounter assumption for the party that CR is based on.
So an NPC mage should be expected to nova with their spell slots (if they have them) and the CR evaluation should be designed to expect that.
So different considerations for PC wizard power expectations per PC level versus NPC CR calculation using the same spell slot chasis that is common to wizards.
That is the default 5e design.
Switching to tracking X/day spells may be more convenient to run in many circumstances but it is not inherently more balanced for CR purposes if NPC mages go full out with the powers on their stat blocks the way noncaster monsters do.
Npc Mages are expected to nova. But they have resources of a PC designed not to nova.
Therefore if you give them full slots, either they never use 50% of their slots or they use cheesey tactics to spend all their slots and TPK the party.
So why give them 100% of their slots if they can't use it without TPK?