Balancing Encounters around a very proficient Necromancer

In a game I am a part of there is a player who considers themself a necromancer. They are fully specced and invested around the spell "Animate Dead". They are very effective and efficient at keeping track of, and controlling their minions, often taking a minute or few for their full turn with 7 fielded minions, each with multiple attacks. The problem is that they are really really powerful. Their control/raise limit is well over what it should be for their level (+9 from a mixture of class abilities and feats/traits that raise CL.) This means they have been able to raise anything that we have come across as at least a bloody skeleton, even adding extra template via use of desecrate. They also pair this with an elevated CL Command undead spell, giving them a large swath of minions to use that are hard to permanently kill.

The setting of the campaign has been the deep darklands, and while we are only level 7, they have given raise to 15HD bloody Firey skeletons. Needless to say, these outperform any martial at the same level.

The party is a small group, with 1 other consistent player who is a Rouge/Arcane trickster, (about as well optimized as they can be with a couple boons to make them stronger) and then a guest player every now and then who is less important and not consistent. As a GM it is getting hard to balance encounters because as the opponents scale up, the party does as well, but the characters do not gain extra capability. No one in the party is upset at the level of power they have, as they generally tend to do different rolls then meat-bag front-line. However they still like to feel useful in combat, and if enemies are too scaled up, they cant hurt them easily.

What are some ways to allow for more balanced encounters? The challenge is providing something that can be a threat to creatures of that capability, while still proving to be a threat to the rest of the party. Im not looking to nerf them unless absolutely necessary. The necromancer has his body hidden inside the skeleton of a large creature, strapped, secured, and hidden, while using shadow projection to command and be safer on the battlefield. AOEs can threaten his body, but its hard to justify direct targeting of his body over the skeleton it resides in, which is also quite mobile. Keep in mind, that the necromancer can raise pretty much anything, so after every encounter, they can potentially get stronger, and can at this point raise (7+5CL x2 = 24 x2 from desecrate = 48) a 24 HD creature as a bloody skeleton, or a 12 HD creature as a bloody flaming (or elemental) skeleton. This is at level 7.