I’m not too familiar with embalming, but if you can understand their process, what chemicals are used during, what the duration of embalming is, and what temp/humidity is preferred you would have your criteria for your makeup air unit at those air changes. I would assume there can be a low air change mode of operation when chemicals are not present or sealed properly - and at that point it would make sense to switch to a secondary system.
As far as energy recovery, slight cross contamination can be acceptable with a simple evaluation - if they provide the leakage rate, hopefully a very low percentage, and if you dilute that into 100% outdoor air, do you come anywhere near toxicity or flammable concentration concerns? Keep in mind your exhaust airstream is nowhere near 100% saturated with chemicals, but this is a simple evaluation that can help remove that cross contamination concern that impedes designers from meeting energy code.