If I recall, it was Safari and older versions of Firefox and IE that didn’t handle it well. And they didn’t just “do nothing”, but actually loaded big scary error pages that would make users think your site is broken.
On my own sites, depending on the targeted users, I might make a different choice. But for a product which could be used on lots of different sites I have to play it safe.
If you’re a developer and want to change the output, you can hook into the bpwfwp_component_callbacks
filter and change the callback used to print the phone markup. Just write your own function to print it with the tel: prefix. You can see how I did this as part of an extension for someone else.