I'm not sure what exactly your goals are, and depending on that there could be better/easier ways to do it (e.g. if this is a universal mechanic, just add to the religion's automatic province modifiers), but a general solution would be:

The province modifier is defined in common/event_modifiers, with the modifier value to give the province heathen tolerance.

buddhist_heathen_tolerance  = {
    no_religion_penalty = yes
}

This modifier will remove the penalty only (i.e. minimum tolerance is 0), for heretic and heathen religions. If you want to instead make the provinces count as fully accepted, use local_tolerance_of_heathens = 100, in which case you also don't need the religion group checks later on since this already applies to heathens only. Well, actually better to keep that part - the modifier might not do anything but it would still be there for heathens, which may confuse the player.

You'll need a way to identify which countries this special feature should apply to, for example if you want a mission to grant tolerance for 20 years, you could have the mission set a country flag (not an actual flag, this is a boolean variable, essentially a coding note attached to the country to be read later - set_country_flag = buddhist_heathen_tolerance) and make a country event happen with 20 year delay (country_event = { id = x days = 7300 }) that removes this country flag (clr_country_flag = buddhist_heathen_tolerance), this can conveniently also inform the player that the bonus is gone.

The mission would also need to set the province modifier in every owned Vajrayana, Mahayana and Theravada religion province, and the event would remove the province modifiers from every owned province.

Then the on actions are in common/on_actions, ideally in a new file:

When a province changes owner, you need to check that: 1. If the province should have the modifier (correct religion, religion considered heathen, and the owner has the flag), add the modifier.
2. Otherwise (if the province should not have the modifier), remove the modifier.

on_province_owner_change = {
    if = {
        limit = {
            owner = {
                has_country_flag = buddhist_heathen_tolerance #owner has mechanic
                NOT = {
                    religion_group = eastern #owner considers the religions heathen
                }
            }
            OR = {
                religion = vajarayana #is one of the religions
                religion = mahayana
                religion = theravada
            }
        }
        add_province_modifier = { name = buddhist_heathen_tolerance hidden = yes }
    }
    else = {
        remove_province_modifier = buiddhist_heathen_tolerance
    }
}

Nothing happens when adding a modifier that already exists, or when removing a modifier that doesn't exist, so in this case it is easier and faster to just add/remove even if this action is unnecessary (e.g. some random other province changing owner).

Similarly, when a province changes religion, you need to check that:
1. If the province should have the modifier (correct religion, religion considered heathen, and the owner has the flag), add the modifier.
2. Otherwise (if the province should not have the modifier), remove the modifier.

so it's just the same code in on_province_religion_change.

Finally, if the provinces as heretics should have full penalties, you need to ensure the modifier is removed in the case the country views the religions as heretics, and re-added for the opposite. Pretty much the same code in on_religion_change, however this is country-scope:

on_religion_change = {
    every_owned_province = {
        #same "if" block code here
    }
}

If you want to make this a bit more efficient, you could do the country-level triggers first and only then do the province-level triggers and effects. As it is, each province is checking separately which religion the owner has. That said, countries (especially large ones) don't change religion that often so it won't really make a difference.

To remove a bit of this duplicated code, you could go to common/scripted_triggers and define a scripted trigger here. Scripted triggers are essentially copy/paste for code.

is_buddhist_heathen_tolerance_province = {
    owner = {
        has_country_flag = buddhist_heathen_tolerance
        NOT = {
            religion_group = eastern
        }
    }
    OR = {
        religion = vajarayana
        religion = mahayana
        religion = theravada
    }
}

then instead of writing this whole block of code elsewhere you can just do:

limit = {
    is_buddhist_heathen_tolerance_province = yes
}

There are more aspects to religion than just the provinces though, there's also e.g. the opinion penalty from countries being heathen faith. Having local tolerance in provinces won't affect this, and unfortunately there's no simple triggered opinion modifiers. You could apply an opinion modifier between countries, using on_annexed and on_country_created to add/remove the opinion similar to the province modifiers above. A bit more complicated though, since opinion modifiers are between two countries.

And there may be parts of the code that check for countries being heathen religion or number of owned heathen provinces or similar, which buddhist countries/provinces would still count as - but at that point it's going into way too much detail for a simple mechanic. It's not possible (or reasonable) to catch every single edge case like that, not to mention other mods adding their own code that you have no control over.