If you can prove that you sincerely believe in the religion you made up 10 minutes ago, then you'd get the same exemption. It's not like they gave a list of religions that qualify for exemptions.
The sincerity of the belief is a measured by the credibility of the claimant in each specific case. They are assumed to be credible by default unless the other party can show glaring inconsistencies. Even then, the guidance notes that people's beliefs change so challenging such a claim is relatively hard.
A sincerely held religious belief is basically a "get out of jail free" card (figuratively) because of the issues you point out. With the preponderance of evidence standard, all one has to do is convince the judge that their belief is more likely to be sincere than not. If one can prove that they go to church on a semi-regular basis, for example, it's nearly impossible to convince a judge that the belief is insincere.
The thing that's causing issues is that many people who are objecting to the Covid vaccines are largely not anti-vax in general, and their reasons aren't really rooted in the philosophy of religious law around vaccines, but the aggressive and sudden push for these particular ones is tripping all of their mental alarms, because aggressive and sudden intrusions by untrustworthy governments are often used to accomplish evil that is extremely contrary to their religious beliefs. A court probably isn't going to be sympathetic to that argument, but I think it's what's happening.
>Even then, the guidance notes that people's beliefs change so challenging such a claim is relatively hard.
It is not relatively hard, it is (or should be) impossible.
My religion stating that I believe in whatever I want to believe and is subject to change at any time is as valid as any other religion, from the perspective of the government. Assuming we are striving for separation of church and state.
Religion never needs to come up in legislation, just like one's favorite tv shows or music.