There are two separate issues that are erroneously lumped together in the site you linked.
The first issue is inclusion in the Catholic Church of children and adults who are anywhere along the spectrum of ability. This is directly the business and responsibility of the Church.
The second, which your thread title addresses is the inclusion of disabled children in Catholic schools. I looked over the website and no where could I find a proposal of how to pay for this. I have two kids in Catholic school now. I pay for the mainstream kids in public school via my local taxes, the disabled children in public school mostly via my federal taxes, my own two kids via tuition and kids who attend our school but can’t afford full tuition through donations.
How would you fund special education in Catholic schools? The schools can’t absorb the cost, they are often just getting by. By a rough calculation, I am already paying for the education of at least three children, only two of which are mine. Asking the parents of the students to subsidize special eduction at the Catholic school would raise tuition beyond what most of us could pay. Asking the parents of disabled children to pay a higher tuition to cover the expenses to educate their children would likely be prohibitively expensive.
The only fair avenue is to pressure the government to extend special education benefits to all disabled children regardless of what school they are in.