Associating a chain to an alignment sequence doesn’t change ChimeraX’s opinion of what the chain's sequence is, since there are various reasons you might what to associate a chain to what might be only a similar sequence.  Nonetheless, what you want to do is pretty useful, so I will try to add support for it in the sequence viewer sometime soonish.  In the interim you can get what you want by running the attached script, which will transfer alignment sequences to each associated chain.  You run the script simply by opening it (“open /where/you/saved/xfer-seq.py”).