Pirc in considered an inferior opening for black mainly because white gets more space and centre control. After Nxe4 Nxe4 d5 Bd3 dxe4 Bxe4, one pair of knights is exchanged, which negates the space advantage a bit (fewer pieces on the board, so space is less important). Moreover, the resulting pawn structure is what can be obtain from the Scandinavian, but white has no development advantage (as he usually gets in the Scandinavian). White centre can later be challenged by c5 or e5. So basically, by allowing this, white loses everything which is responsible for the typical + for him in the Pirc. I would not unequivocally say that black is better in this line (white should be able to equalize), but allowing this is certainly not in white's interests.
And of course, Bxf7+ Zwischenzug is just bad, as black gets two bishops and utter control over light squares eventually.
Update: Because my last statement turned out to be controversial, I checked the lichess database (2200+) of this exact position after Nxe4.
Nxe4: played 13 times, 38% 1-0, 31% =, 31% 0-1 (+5=4-4).
Bxf7+: played 6 times, 17% 1-0, 33% =, 50% 0-1 (+1=2-3).