Hey Ranga,
Yes, it is possible to specify a custom Machine SSL Certificate during the deployment of vCenter, but VMware doesn't provide a built-in way to inject it directly in the deployment wizard. The usual approach is to deploy vCenter first, let it generate its default self-signed certificate, and then replace it afterward—which, as you mentioned, can introduce temporary SSL verification issues unless you trust the VMCA.
If you're looking to avoid that insecure phase entirely, one way is to preload your custom certificate into the vCenter appliance before first boot. You can do this by mounting the installation ISO, modifying the configuration files inside, and injecting your custom root CA and machine certificate into the appliance before it even starts the deployment process. This is not an officially supported method, but it has worked in lab environments.
Alternatively, if automation is key for you, another option is to script the deployment using PowerCLI or vCSA CLI, followed by an immediate certificate replacement via the vSphere Certificate Manager or API calls. This ensures that as soon as vCenter comes online, it already has the correct SSL certificate applied, minimizing the exposure to self-signed certificate warnings.
It would be great to know what deployment method you're using