Since children with EHCPs are entitled to go to the school that best meets their needs, this statistic is probably indicative of a belief that the school isn’t best suited to those children, but it isn’t indicative of how well they meet the needs of the children they have with SEN.
That's not what the law says. Children with EHCPs must go to schools that meet their needs, but there parents aren't entitled to placements at the schools that "best" meet their needs. Further, if parents of children with EHCPs prefer a mainstream place (including mainstream academies) then their preference must be met unless placing the child there will be incompatible with the efficient education of other pupils and there are no reasonable steps that can be taken to overcome the incompatibility.
So there are are major questions around why that statistic is so low. At the time covered by those statistics, it looks like in practice they had, at most, two children with EHCPs. As you have pointed out, for some children with EHCPs the Michaela régime sounds good. Also, putting a child with serious SEN into a newish school tends to be very attractive anyway because it will be very small when the child arrives and they will have time to get used to it as it grows. So it seems likely that quite a lot of parents of children with EHCPs put Michaela down as their first preference but don't get places there. Alternatively, they do get places but their children end up leaving. What's going on there?
Further, Michaela isn't apparently putting forward children for EHCPs or supporting parents who do so at anything like the same rates as other comparable schools. I'm sure people will claim that that is because it's wonderful, but you have to wonder whether it's to do with not wanting local authority oversight and having to comply with the requirements for special educational support in the EHCP when they doesn't fit conveniently into their system. Or whether, again, they simply ease the EHCP candidates out before they have to meet their needs properly and make those inconvenient reasonable adjustments.