In theory, it counts, and since you have to list your entries and exits and let the tool calculate your days for you, it will be considered in your physical presence total.
The caveat is that IRCC can't always validate your status during these days (in opposition to pre-PR days as a student or worker) , and we've seen reports of applications being returned to applicants who relied on these visitor days to reach the 1095 days threshold. Example here :
https://www.canadavisa.com/canada-immigration-discussion-board/threads/citizenship-application-cancelled.860943/
So, yeah, you're absolutely eligible with those days, but the onus is on you to prove your physical presence. If you can convincingly prove every single day you were in Canada as a visitor, send that justification with your application and are ready to face a potentially lengthier application processing before your physical presence turns green, by all means, but there's a significant chance you'd get to the finish line earlier by simply waiting a bit more before applying, have these days as an additional buffer that you wouldn't need to reach the threshold, and make things easier for you and for the IRCC officer working on your application.