I really like the names you’re considering.
I agree about the flow of Margot Elsie not being “perfect” - it’s the O to the E that isn’t super satisfying to say. Keeping in mind, I always think better to honour than go for a less meaningful but entirely rhythmical name - so it may be at the end of this, Margot Elsie is still the best pick - they’re both beautiful and very spunky, cute-vintage names and its only a small bit of imperfect flow, it’s not a deal breaker in any respects. Also, it likely sounds a lot better with the last name in play - sing-song sweet!
But if it really isn’t sitting right for you:
As a wildcard first option, how about Elspeth or Elsbeth as a first - may still get Elsie as a nn but isn’t strictly Elsie in first. I just think Elsbeth (I would pick Elsbeth so can also use Beth) would flow so well to a single syllable W last name, with maybe Margot or Mabel in second spot. Or there’s Eliza Mabel W? Eliza and Elspeth/Elsbeth both related to Elsie so still an honour.
Could you go Margaret Elsie W nn Margot/Maggie/Peggy? Or you could go for Margot Elise if Elise is enough of an honour to Elsie - it does flow better, I think. Same for Margot Elisabeth.
Another option would be Eloise Mabel W - with Eloise as your Elsie honour.
I don’t think Mabel Elsie helps with the El to El. What about Sabella as a first - then you get your Mabel sound and your honour to Elsie (with Sabella being a variation of Elizabeth, and Elsie being a diminutive). Eg Sabella Margot W. Or of course, Margot Sabella with Sabella being your Elsie nod.
Willow Elsie W sounds like it would flow very well. But if you’re off Willow, maybe Autumn Elsie, Philippa Elsie (Pip/Pippa), Harriet Elsie, Maeve Elsie, Marion Elsie, Helena Elsie, Anwen Elsie, Madeleine Elsie, Florence Elsie.
Look forward to hearing if any of these help but I would only change Margot Elsie if it’s really bugging you and nothing anyone says changes that!