They do know that one of the Converted is a Sewaddle. And Sewaddle is not native to Santalune Forest. They'll likely be prioritizing Allie though. (Blending in might work though. Grunts are intelligent but not incredibly intelligent.)
They're prioritizing Allie due to the fact that she's powerful but still has one evolution left. They want to experiment on evolution and how it affects a Converted. However, Harper is impatient and wants to experiment on the power portion of things now, making Allie a suitable candidate due to her already having some power.
Also, anyone who is RPing an Admin/Top Grunt/Scientist may control Grunts as NPCs. (Except for Grunts who are being RPd by a user.)