There are two accounts in my Mail app, one for me and one for my wife. Each of us has our own Trash. The icon looks like a trash can, in contrast to the On My Mac icon, which is generic. Our deleted emails go into our individual Trash, and nothing goes into the On My Mac trash. I have no idea why this happens but it seems to parallel your observation to some degree.
Hover the mouse over your account mailbox. When you do this, do you see the > symbol? If so, click it to reveal extra mailboxes.
macOS 11.1, iMac Retina 5K 27-inch, late 2014, 3.5 GHz Intel Core i5, 1 TB fusion drive, 16 GB RAM, Epson SureColor P600, Photoshop CC, Lightroom CC, MS Office 365