[Mrs. Clay] has abilities, however, as well as affections; and it is now a doubtful point whether his cunning, or hers, may finally carry the day; whether, after preventing her from being the wife of Sir Walter, he may not be wheedled and caressed at last into making her the wife of Sir William.

Personally, I think JA was saying that this is not as unequal a "contest" as it might look on the outside. Outwardly, all the advantages seem to be on Mr. Elliot's side, as you point out. However, we are told that Mrs. Clay has abilities as well as affections. The point is that she is insidious - she slides in while nobody is looking! Look at the change in Sir Walter's attitude towards her in the comparatively short time (2 months?)they were together, even though he never went so far as to consider marriage.

I think sheer habit and settled routine would be on Mrs. Clay's side - she would be a pleasant companion, after all, and Mr. Elliot is no longer a boy - I don't think he would want change for its own sake. IMO he might eventually come to feel that he could do worse than marry her. He seems to have enough money for the both of them, he will achieve a title without any wife's help, he knows Mrs. Clay is probably fertile, having had 2 children already. Come to think of it, what would happen if Mrs. Clay were to become pregnant? Would Mr. Elliot marry her (it would need to be *before* the baby was born to make it legal)in hopes of a son?