Well, yeah. It totally depends what story they replace that one with. There's always something more ridiculous, as well as something that makes perfect sense.
Here, I've got one that falls somewhere in between. It's ridiculous in that it introduces more moving parts and would be really confusing, and would make certain characters' motivations in past stories kind of weird, but here we go...
There was never a Magda, or if there was, the real one never made it to Wundagore Mtn.... Magda was either a memory insert via magic, or was duplicated/possessed before she got to the mountain. Instead, the twins' mother was a time-travelling Morgan Le Fay, who came to the right future time to consummate a special relationship/ritual with the Elder God Chthon in his place of power. The twins' powers are and have always been essentially supernatural in nature, especially Wanda's (although who knows what untapped potential Pietro might turn out to have once all this is revealed), in the same way as those of the Brothers Grimm or the Puppet Master's clay figurines. After giving birth, Morgan made herself appear to die and returned to her own time. Wyndham, the High Evolutionary, knew there was something weird about the twins, so he kept them in suspended animation to study them for a period of time, and ended up performing some genetic manipulation to make it appear that they were active X-gene bearing mutants, a group he'd been (retconned into) studying in his quest for the keys to evolution, before passing them off to the Maximoffs and their Roma tribe.
Of course, besides being convoluted to the degree of silliness, the above would kind of result in the twins being the Anti-Christ, but there you go...