No.
A has more X, compared with B.
[ independent clause] comma "non-independent clause"
joining these two with a comma is not a good idea. If you are trying to join complex sentence structures try starting with...
Compared to that of A..... comma, B has got 29 percent more X. [using compared to as an introductory clause, you can't go wrong with the comma... after it]
A had more x when compared to B. A little better?
A had more x than B. Simple and beautiful.
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