`--set '.base = ...'` fails with "field `base` must be empty for YAML validation"

### Description

Using `--set '.base = ...'` fails with `limactl create`, `limactl start`, and `limactl clone`.

```bash
# Create a simple test template
cat > /tmp/test.yaml << 'EOF'
images:
- location: https://example.com/test.qcow2
arch: x86_64
EOF

# Test 1: limactl create - FAILS
limactl create --tty=false --name=test --set '.base = ["template://alpine"]' /tmp/test.yaml

# Create instance to start/clone
limactl create --tty=false --name=existing-instance template:default

# Test 2: limactl start on existing instance - FAILS
limactl start --tty=false --set '.base = ["template://alpine"]' existing-instance

# Test 3: limactl clone - FAILS
limactl clone --tty=false --set '.base = ["template://alpine"]' existing-instance cloned-instance
```

All three commands fail with variations of:

```
FATA[0000] field `base` must be empty for YAML validation
```

This might be similar to #3741.