I am referring to entire product. One limitation with Atmega329 is the small flash size. I fear the day when customer asks for more features and flash size runs out. AVR MCUs with larger flash size costs significantly more. Not so with PIC.
So just charge them the 'significantly' more chip cost when you quote them the price for their 'more features' request. Again you aren't selling them chips, your selling them the total value you add.
I guess we need a more details on your specific business model and specific products you sell to offer solutions to your dilemma.