this sounds like a complicated case, and the facts are also in dispute. it's not going to be clear what the right answer is until the facts come out in a trial. but, my understanding of the general legal question is this:
is waxing a "general service" or a "specific service"? it might seem like it's a specific service, but there's some ambiguity if it's a general package.
a general service is something like picking something off of a menu. so, if you go into a restaurant and order the #2 special, denial of service on enumerated and analogous grounds would be a rights violation. but, if you order a #2 special with a list of specific modifications, that is a specialized service, and the owner has the right to refuse.
if the facts in the end demonstrate that this woman walked in and requested a wax job off of a menu, i would uphold the idea that this is discrimination - and i would not take the religious defense seriously. i don't think that citing religious observance is an excuse to deny service that is advertised; religion is the reason we have human rights in the first place. if the owner wins this case by citing "religious freedom", then that is just some kind of orwellian destruction of the concept of human rights - that would be upholding the right to discriminate, which is upholding the right to ignore human rights.
but, given that waxing services are widespread, i have a hard time understanding the claim to a $50,000 payment as a consequence of that discrimination. i would think that the complainant would have to demonstrate more concrete fiscal costs to be awarded a claim of this sort, or tie it to some kind of lost revenue. she's basically asking for $50,000 because somebody hurt her feelings.
it's going to come down to a bias in the judicial process, as these things generally do. but, even if she wins the argument, i don't think she wins the claims. and, it's consequently one of those weird scenarios where the judge would be justified in granting her the point - but forcing her to pay costs, anyways.
https://windsor.ctvnews.ca/human-rights-application-launched-against-windsor-body-waxing-business-by-transgender-woman-1.3925911