Bottom line: If I do not believe a company has my best interests as a customer at heart, then I would be a fool to stay with that company. That is the net net of this conflict of interest.
The conflict of interest is the future of TypePad as a source of ongoing revenue vs a large number of small self-hosted MT installations with multiple authors who would otherwise be TypePad customers.
Have I mentioned the two different markets/audiences that 6A should be aware of and working with?