Well, on the hearthstone wiki one of the notes under magnetic reads thus:
“If you use a Magnetic card to upgrade a mech, that upgrade is treated as an enchantment, not as a transformation. So, for example, if the mech is silenced or returned to the hand, it loses all the effects it got from the magnetizing.”
For me there has never been any ambiguity about the mechanic. If people don’t understand how it works they can’t blame Blizzard for their lack of understanding, the information is out there if they want to find it. Ignorance isn’t really a valid excuse.
The intuitive sense you mention would be pretty silly to be honest because magnetic is a pretty powerful mechanic already. If the combined minions were still treated as 2 (or more) separate entities combined then there would be no real viable interaction with silences being used on them and returning them to hand would theoretically divide the minions back up before adding them back to the players hand not only allowing them to just replay the magnetizing combo (which is quite a scary prospect if Zilliax is involved) but it would also allow players to magnetise cheap minions early to dominate the board and then, in the late game, break them back up to combine with bigger minions to created more combos. Big magnetized minions would effectively be immune to most removal with the exception of polymorphing effects and effects that reduce health/attack, of which there are very few in the game at the minute.
The intuitive sense could, effectively, make an already powerful mechanic, pretty broken