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I can only speak to r_l in this case, but navsat_transform_node was designed to permit moving from indoors to outdoors and vice-versa. The problem, as you said, is generating a consistent coordinate frame between amcl and your EKF instance.
If it were me, I'd try fuse instead (it's been released for ROS 2). You'll still need navsat_transform_node from r_l, but fuse will let you fuse both the output from navsat_transform_node and amcl. Just enable differential mode on one or both of them. There could be some experimentation required; I don't think I've seen anyone try this particular setup yet.
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