I have a lot of thoughts on what you are talking about. Here are some of my thoughts. I tried to put them in some sort of order but mostly failed.
1) Conditioning to me is always sport specific. Meaning I know guys that have mat conditioning in BJJ but could not jog a mile if you had a gun to their head.
1.5) I can do Crossfit workouts if I don't take the intensity all the way to kill level.
2) My BJJ training is very interval based so I get a ton of intervals every time I train.
3) When I started training BJJ I was more of an endurance athlete (I had been doing triathlons for 4 years at that time) than strength based. I feel like I had a lot better base to build my mat conditioning on. This was also when I was doing Crossfit workouts. That was probably what helped me progress so quickly in the beginning. I could grapple and then go again without even breathing hard. Now it is a little more of a struggle.
3.5) In all the years that I did Crossfit WOD's, even some of the hour long ones, I never pushed it so far that I got sick. I have thought about that a lot and have wondered if I pussed out on some of those workouts and now I think I probably saved myself some wear and tear. There have been a couple of times training BJJ in the last year where I thought I was going to die and my instructor had me go one more round. The next two days after that have always sucked.
4) Looking back at my endurance training it mostly was running all well under 80% of MHR.
5) I have decided that when my foot is healed I am going to start running and rowing at that 80% or less MHR. I was influenced by Joel Marions stuff after reading about him in a thread in the fighting section.
I have more crap rolling around in my head. Just let me know if you want me to expand on any of these ideas.
What we think, or what we know, or what we believe, is in the end, of little consequence. The only thing of consequence is what we do. -John Ruskin