Only if you have 256 colours, you don't waste precious RAM in a chunky mode.
You don't waste RAM, but you waste computing power and bandwidth when manipulating the display. Even with a blitter, modifying an eight-bitplane display requires (unless you are lucky) eight separate accesses to the RAM, once per bitplane. Chunky requires only one. Plus, you save all the computations to extract individual bits.
When they eventually did AGA they probably realised that with now 256 colours they could have done a chunky mode without wasting RAM or bandwidth but they just considered it too much work and decided to do just a lazy patch job of ECS changing only the screen DMA engine.
Well, I wouldn't generalize it by that, especially "they". As far as the engineering department was concerned, people there were well aware that a major revision of the hardware architecture was urgently necessary, but CBM was short of money and resources, and a management vision.
At that time they would not only have had to add chunky gfx but also 16 bit audio and a 32 bit blitter to have kept it competitive.
A couple of these ideas (and much more) was planned for AAA, but CBM went down under just before this was completed.