Yes. Steem Engine and SMTs are different things altogether. Some SE tokens might shift to SMTs since they really do fit into the box of mini-steems. However, any projects that are looking to expand at all by utilizing Smart Contracts are going to be SE.

SMTs provide for specific activities which are accounted for under the resource credit system. Anything that does not fit into that is a SE project.

An example would be NFTs or a token that requires recurring payments.