To be fair I suspect the thing with Revan and the Exile was more Lucasarts doing than Bioware or Obsidian's. By tradition I think the "light side" endings to most of their games that have such things are the ones considered canon. That is whatever passes for canon in the Expanded Universe.
Regardless, Shepard's gender, background and who she or he diddled is hardly likely to come up much. In DA2 the Warden was mentioned half a dozen times or more and I'm pretty sure gender pronouns were only used a few times and race referred to once in passing.
None of which would make it difficult to write a Mass Effect story set centuries after Shepard died. They just have to keep an eye on their word budget and work around it for the most part. They've already done some of the legwork with that "stargazers" epilogue by establishing that in the indeterminate future, Shepard will just be referred to as "The Shepard" and most of the details are "lost in time". That last part is more credible than you might think when you consider that no matter the ending choice, civilization just fell. When that happens, accurate record keeping and the preservation of old documents tends not the be a priority for a while.
Of course logically all one need to in theory is ask a Geth (if they're still around) as it's a fair bet they'd remember everything they ever knew of Shepard, but that's neither here nor there.