For example, "sleeping in public places not meant for human habitation" would include anyone who has ever taken a nap in the airport, even one time.
When the piece starts out with an obviously bogus definition, there's really not much point in going through it point by point. It has zero credibility from the start.
Other sources (easily found by Google) suggest that up to 2/3 of the real chronic homeless population has problems with alcohol and/or other substances
No, I'm not. I'm pointing out that the definition given in your "factual" source, to wit "sleeping in public places not meant for human habitation" is ridiculous on its face.
Ever slept in class? Then you've been "homeless", according to your source.
I really don't mean this as a personal attack, but rather as a suggestion: you should learn to tell the difference between factual research and advocacy pieces. Your source is the latter. There is absolutely nothing wrong with advocacy, but one must take it with a grain of salt. When it starts out with a straw man definition (as does your source), perhaps a boulder of salt would be preferable.
"Furthermore do you have source material that calls the numbers used in the article into question"
https://www.ncbi.nlm.nih.gov/books/NBK138716/
Mental illness:
"An earlier literature review on physical and mental disorders among those who are homeless (Martens, 2001) cited reports that found that anywhere between 25 and 90 percent of people who were homeless had a mental disorder. A review by Toro (2007) suggests that 20 to 40 percent of people who are homeless have a serious mental disorder, with 20 to 25 percent having depression and 5 to 15 percent having schizophrenia. In their introductory review, Greenberg and Rosenheck (2010a) note that estimates are that between 20 and 50 percent of people who are homeless have serious mental illness (SMI). Research reviewed by McQuistion and Gillig (2006) also indicates that between one third and one half of people who are homeless have SMI."
Substance abuse:
Another Midwestern study recruited subjects who were homeless from food programs and shelters (Forney, Lombardo, & Toro, 2007); here, 77 percent of men (n=161) and 55 percent of women (n=57) met criteria for a substance use disorder. Velasquez, Crouch, von Sternberg, and Grosdanis (2000) found that among a sample of 100 clients of the Service of the Emergency Aid Resource Center for the Homeless project in Texas, 60 percent reported use of illicit drugs in the prior 6 months. In an analysis of NESARC data for people who had experienced an episode of homelessness since the age of 15, 74.2 percent of respondents also met criteria for a lifetime substance use disorder; only 30.5 percent of those who had always been domiciled met such criteria (Greenberg & Rosenheck, 2010a).
There are many other citations in this report.