When Watanabe added the native implementation (was in 2013 with the 2a75a35) he did things with his usual care, even adding a guard to the NATIVE_RULE, that is he wrote below the Jam implementation of the rule

if [ HAS_NATIVE_RULE sequence : transform : 1 ]
{
    NATIVE_RULE sequence : transform ;
}

In my review I removed both the guard and the Jam rule, trusting that the interpreter always has the native version.

But if there were a possibility that an old engine was dealing with the new sequence.jam this creates a problem since the old engine without the implementation of the rule in Jam (which I removed) and the guard on NATIVE_RULE (which I also removed) would encounter an error.

So if you think this might happen then please use 6abf2af which restores both.

The reason I removed them is that when Kniazev implemented native unique (in 2023, see d349465), he didn't use any guard for NATIVE_RULE.
And this leads me to think that the case of an old engine with new jamfiles should not occur, and probably Watanabe was too scrupulous or was concerned with ensuring the version of the native transform rule was = 1 (I will return to this aspect when I deal with the guard, i.e. the HAS_NATIVE_RULE.)

And this leads me to think that the case of an old engine with new jamfiles should not occur, and probably Watanabe was too scrupulous or was concerned with ensuring the version of the native transform rule was = 1 (I will return to this aspect when I deal with the guard, i.e. the HAS_NATIVE_RULE.)

Once upon a time, when Watanabe did this, such mixing was a constantly occurring headache. As the b2 binary would be installed by system package managers. But people, as in Boost devs, would run that instead of the in-tree one. I resolved this though when I made b2 search for the "attached" build jam files instead of relying on the search path. So, yes, it's safe to remove the native rule checks. They are pointless at this time.