Trainyard had a mechanic where if you allowed all three primary colours to mix (eg. a secondary plus the other primary, or two dissimilar secondaries), you'd get a murky brown colour which was effectively dead weight. You couldn't get rid of it once you'd made one, so you had to plan your moves carefully to ensure the wrong colours never came in contact.
A mechanic like that might be a way to add escalating pressure, creating blocks you can't eliminate (or maybe only a tertiary bomb can eliminate them?) and restricting your moves.
Another angle you may want to investigate is nerfing the tertiary bomb, as the current version sounds quite powerful considering it can be made in just two steps. Some possibilities:
Tertiary bombs can only destroy (chains of) adjacent blocks, so there's some strategy to arranging them before detonation.
Or they can only destroy a muddy brown block, as a way of recovering from a previous mistake.
Tertiary colours aren't bombs, they just turn back to their dominant primary if mixed with that primary one more time (diluting the other primary out).
Combined with the above rule about muddy browns, primaries are your safest colours because they blend with most things, and compound colours are liabilities. Tertiaries become a way to remediate a secondary back into safe primaries again - so the strategy becomes about managing how many compound colours you have in play at once.
A third angle is to restrict the moves the player has available. For example, if two colours share a primary, but aren't similar enough to mix into a single block, they "stick" together when they touch, until one of them changes colour or is eliminated.
This bars one of the avenues for merging the block with another, since now it has this other colour in the way. And it can stick out like a shelf, interfering with the transport of blocks in the adjacent row/column.
If the player isn't careful, they could turn their playfield into a big tarball of almost-but-not-quite matching colours, limiting their flexibility to respond to new situations.