I'm not sure what you mean by "custom methods", but I'm not saying they have bypassed the e2e encryption - I'm just saying that they technically could.
And as for why they would do that, they might get compelled by a government to do it secretly. As far as I know that hasn't happened yet but I see no reason it couldn't and it would take a whistleblower to find out.
> Security wise it's amazing. If a company's admin cannot take your data it's excedingly hard for a hacker to do so.
I agree, it is the best option available. But Apple/Meta are technically lying when they say it's impossible for them to read your messages.