That the outer NDB is about 6 km from the runway threshold instead of 4 is irrelevant. I doubt such a so-called "standard" would exist in any regulation worldwide. As PJ2 explained, an approach has to be prepared using a specific chart on which all the necessary information is printed.
A possible QFE / QNH confusion appears remote since the crew was certainly "current" on the russian altimetry procedures and had a recent experience. It seems an erroneous reference pressure (QFE most probably) like an error on the next to last digit would be more consistent with the position of the first tree hit (assuming that a correct vertical speed was used).
Obviously, such an error could have multiple sources. One of them could be bad radio transmissions. By the way, ATC reported the crew had problems understanding numbers. Whilst the captain was said to be a fluent russian speaker we don't know who was tasked with radio transmissions.
Just a theory...
DJ