Whatever the assembled experts on Pprune or in the exalted halls of power at AENA might think, the 767 crew clearly thought the A340's actions compromised safety margins. When in doubt, there is no doubt - particularly when 100s of lives are at stake.
Personally, I would not enter an active runway with someone on short final whatever ATC clear me to do, and I wouldn't cross a runway if I couldn't see it. I trust my judgment before that of someone drinking a cup of tea, safe in their tower a few 100 metres away.
I say that having been cleared to land at 25R in BCN at 100' because they 'forgot' us and been cleared to land when reporting at the hold for departure. Nothing surprises me when it comes to Spanish airports.
Ironically, the great challenge in Spain is getting airborne despite the huge spacings they require between traffic!
Incidentally, I've flown into BCN dozens of times but never seen 02 in use, but taxiing for 25L we have always been cleared to cross 02/20 by GND, not TWR. When the runway is active things might be different - or so one would hope.