More to the point, there is still chromosome structure when the cell is normal mode, expressing proteins instead of replicating itself. It's just it is spread apart, probably like a pop-up book where "pages" will snap open and become accessible for transcription as part of gene regulation and other times will be folded up so genes in that section aren't expressed.

Some of the reason it is tough to make GMO products that are really effective is that it's not enough to put a gene in and have it expressed a little, you want to have it expressed a lot. For instance the first version of Golden Rice produced Vitamin A but not enough to matter, it took several years to make one that expressed the genes strongly enough that it made significant amounts of Vitamin A.