gencert with -initca ignores most config arguments

### Context
Creating a certificate authority using a two-tier key heirarchy. Root here is used ONLY to generate a new CA, and is stored in a 'secure' location *under my bed*

### Usage
`cfssl gencert -initca -profile intermediate -config config.json -ca root.pem -ca-key root-key.pem ca-csr.json`

### Expected outcome:
Generates a new CA certificate signed by the Root certificate, which includes the options specified by the profile "intermediate" in `config.json`

### Actual outcome:
Generates a basic self signed certificate as if no options were specified.

### Workaround 1
Generate and sign the certificate as two separate steps i.e.
`cfssl gencert -initca csr.json | cfssljson -bare ca`
`cfssl sign -profile intermediate -config config.json ...`

### Workaround 2
Including
```
"ca_constraint": {
"is_ca": true
}
```
in the config.json profile for a certificate has a similar outcome.

### Notes
This can be confusing to understand, especially considering the documentation makes no mention of keys invalidating other keys. In this case, I was unaware that my config options were being ignored until inspected the certificate directly. Would be handy to have a warning if arguments are discarded.

Thanks! :)