AIEC resides in tissue, they can invade through the peyer's patches and epithelial cells of the intestinal wall, they invade macrophages and replicate inside them. They bind to their m cell too and stick to the intestinal wall with biofilms. It's a trojan horse bacteria.
You can somewhat kill them with antibiotics, they're just extremely resistant. Some of the macrophage penetrating antibiotics kill them in vitro, which is probably why some people with crohn's disease, especially the ones with ileum disease, feel better for a while, until they run into resistance.
I have posted studies about antibiotic susceptibility of AIEC in the past if you want to see them.
If the bacteria was just a lumen commensal I don't think people with crohn's disase would have transmural inflammation or fistula, AIEC is highly pathogenic and is very capable of invading tissue.
There's other bacteria capable of doing this, MAP is capable of doing this too, and so is Campylobacter concisus.