First, I'm not presenting myself as an expert here to the degree of some here. Though I did coach rowing for 10 years without a bunch of certifications, etc.
That out of the way.
There's no evidence that I know of that it does. When you periodically ramp up intensity beyond the purely aerobic into threshold/VO2 range your aerobic system is still going full-blast. It's still getting training stress, and it's still going to adapt. The only way I'd speculate that mixing intensities would harm aerobic adaptation is if the effects of the intensity impair the quality and volume of your aerobic training either within the same session (poor quality at the end of a 90-minute run) or across sessions (not being able to complete tomorrow's 90-minute tempo run because you're wiped out from today's mixed-intensity run).
You should be able to recovery back to "tempo" after dipping into higher intensities. You mentioned doing intervals at like 10K pace within a long run. That's a difficult workout. But you should be able to recovery back to tempo pace after a mile at 10K pace. That's a difficult workout. The kind you'd want to take a few days to recover from if there are a bunch of those 10K miles. If you can't recover back to tempo, then you're just don't nearly have the fitness to pull it off. But it sounds like you have a good "base" of zone 2 running. You should be able to spend some time in zone 3. Even 4. And then drop back to 2 without a lot of drama.
I'd say trust the coach. It's OK to question the advice, and get the rationale for it. But there's nothing you're describing that sends up any sort of red flags that they're suggesting something wrong.
That out of the way.
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Can you say why mixing intensities doesn't hurt aerobic adaptationThere's no evidence that I know of that it does. When you periodically ramp up intensity beyond the purely aerobic into threshold/VO2 range your aerobic system is still going full-blast. It's still getting training stress, and it's still going to adapt. The only way I'd speculate that mixing intensities would harm aerobic adaptation is if the effects of the intensity impair the quality and volume of your aerobic training either within the same session (poor quality at the end of a 90-minute run) or across sessions (not being able to complete tomorrow's 90-minute tempo run because you're wiped out from today's mixed-intensity run).
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But maybe its wrong and lactate gets eliminated quickly so doesn't matter for the training stimulus?You should be able to recovery back to "tempo" after dipping into higher intensities. You mentioned doing intervals at like 10K pace within a long run. That's a difficult workout. But you should be able to recovery back to tempo pace after a mile at 10K pace. That's a difficult workout. The kind you'd want to take a few days to recover from if there are a bunch of those 10K miles. If you can't recover back to tempo, then you're just don't nearly have the fitness to pull it off. But it sounds like you have a good "base" of zone 2 running. You should be able to spend some time in zone 3. Even 4. And then drop back to 2 without a lot of drama.
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Now I want to add in intensity but am not sure about the best way to do it...I'd say trust the coach. It's OK to question the advice, and get the rationale for it. But there's nothing you're describing that sends up any sort of red flags that they're suggesting something wrong.