Test scenario:

enable the copr repos @pki/master and @freeipa/freeipa-master-nightly, install freeipa-server-dns
do the first step of IPA installation with an externally-signed CA: ipa-server-install -n ipa.test -r IPA.TEST -a Secret123 -p Secret123 --setup-dns --forwarder 10.11.5.160 --external-ca --external-ca-type=ms-cs --external-ca-profile=1.2.3.4:100 -U
call uninstall because you realize the wrong profile was used: ipa-server-install --uninstall -U
The directory /root/.dogtag/pki-tomcat/ca is still present and contains left-overs:

1. ls /root/.dogtag/pki-tomcat/ca
   alias password.conf pkcs12_password.conf

re-do the first step of IPA installation with a different profile: ipa-server-install -n ipa.test -r IPA.TEST -a Secret123 -p Secret123 --setup-dns --forwarder 10.11.5.160 --external-ca --external-ca-type=ms-cs --external-ca-profile=1.2.3.4:200 -U
The installation fails because the directory /root/.dogtag/pki-tomcat/ca already exists:

Configuring certificate server (pki-tomcatd). Estimated time: 3 minutes
[1/16]: configuring certificate server instance
Failed to configure CA instance
See the installation logs and the following files/directories for more information:
/var/log/pki/pki-tomcat
[error] RuntimeError: CA configuration failed.
CA configuration failed.
The ipa-server-install command failed. See /var/log/ipaserver-install.log for more information

Content of /var/log/ipaserver-install.log:

INFO: Storing registry config: /var/lib/pki/pki-tomcat/conf/ca/registry.cfg
DEBUG: Command: mkdir /root/.dogtag/pki-tomcat/ca
DEBUG: Command: mkdir /root/.dogtag/pki-tomcat/ca
ERROR: FileExistsError: [Errno 17] File exists: '/root/.dogtag/pki-tomcat/ca'
File "/usr/lib/python3.9/site-packages/pki/server/pkispawn.py", line 594, in main
deployer.spawn()
File "/usr/lib/python3.9/site-packages/pki/server/deployment/_init_.py", line 5867, in spawn
scriptlet.spawn(self)
File "/usr/lib/python3.9/site-packages/pki/server/deployment/scriptlets/security_databases.py", line 46, in spawn
deployer.init_client_nssdb()
File "/usr/lib/python3.9/site-packages/pki/server/deployment/_init_.py", line 972, in init_client_nssdb
pki.util.makedirs(
File "/usr/lib/python3.9/site-packages/pki/util.py", line 118, in makedirs
os.makedirs(path, mode=mode, exist_ok=exist_ok)
File "/usr/lib64/python3.9/os.py", line 225, in makedirs
mkdir(name, mode)