Something does not sound here. This most likely could and should be a method on it's own, so we could add tests just for this method

something like

log.Debugf("Modifying endpoint: %v, changing record type from %s to %s", ep, ....)
if ep.RecordType == endpoint.RecordTypeCNAME && strings.CutPrefix(k, disableAliasPrefix) {
   epModified = .....modify me...
   or 
   epC = ep.DeepCopy()
   epC.RecordType = modifyMe(......)
}

Make sure not to use &endpoint.Endpoint{}, but methods available in the package. This will create tech debt for us.

I'd say it should be clone or similar function in Endpoint package, to make sure we do not mutate original

My opinion, we will benefit to have a generic,centralised method on Endpoint object for all annotations that contains booleans like true/false

something like

func (ep *endpoint.Endpoint) GetProviderSpecificBool(key string bool) bool {
	val, ok := ep.GetProviderSpecificProperty(key)
	if !ok {
		return false
	}
	// Normalize whitespace and case; accept common truthy values
	v := strings.TrimSpace(strings.ToLower(val))
	switch v {
	case "1", "t", "true", "yes", "y":
		return true
	case "0", "f", "false", "no", "n":
		return false
	default:		
		return false
	}
}

That does sound like a good idea.
However, in this change we’re going to use values other than just true/false, as @mloiseleur mentioned, and I’m a bit concerned that introducing a generic, centralized method here would make the scope of this PR too large.
I’d prefer to handle that refactor in a separate PR that can apply the change across the whole codebase. What do you think?

Ok

Use constants instead of strings for "true".