How does seeing alters as Entirely separate from you couse harm?
(I'm not trying to start beef I just wanna know coz I'm curious and bored
I have a draft about this somewhere but I'll respond to you until I post that.
Alters are dissociated states and dissociation is what makes alters separate from one another. Dissociation is the process of disconnecting from your thoughts, feelings, surroundings, etc... yourself and everything as a whole. This is something everyone does to some degree, but pwDID (and other disorders further on the dissociative scale; PTSD, CPTSD, BPD, OSDD, etc) experience dissociation in a maladaptive way. Like a coping mechanism that becomes unhealthy.
By viewing your alters as something entirely separate from you, you are causing further disconnection from yourself therefore worsening dissociation for yourself/that alter. Alters who are uncomfortable using a name that isn't their chosen one, are disconnected from their physical appearance or focus on internal appearance, find more enjoyment in "innerworld" than real world, refer to their body as "the body", and other things like that which cause distress if not fed into have an unhealthy level dissociation. This is normal for pwDID; it is a dissociative disorder after all, but it's not good. Encouraging this and feeding into it forever just because it feels better than working on recovery is causing harm to yourself.
I like to compare it to MaDD. Day dreaming can be normal, people do it all the time. When it becomes maladaptive is when it starts to become unhealthy. Someone who is using MaDD as a coping mechanism may not want to focus on recovery because it's hard and living with it just feels easier. But learning to move away from that unhealthy coping mechanism, no matter how difficult it is, is necessary in learning healthy ways to cope and handle things in life instead of resorting to escapism in the same way of relying on dissociation.
Allowing your alters to have some level of individuality isn't seeing them as separate for all people. This is why certain things like Simply Plural, naming alters, tracking switches, etc can hurt someone instead of helping them. Does this make it counter productive for all people? No! That part heavily depends on the person, and some level of individuality can be helpful for someone. If that individuality leads to feeling distress when acknowledging you are one physical person at the end of the day, that is when it becomes unhealthy.
Not everyone is at a place where they can acknowledge their alters as part of them, and that's okay. Dissociation comes with the disorder (obviously..) and recovering from that takes time. Viewing your alters as something entirely separate from you shouldn't be encouraged in the long run though, because it's not helping even if it feels best in the moment. Even functional multiplicity requires some level of integration and acknowledging yourself as parts of one whole.
Hopefully this makes some sense.
TL;DR: Feeling separate from yourself is dissociation, encouraging that worsens the dissociation. Individuality isn't the same as seeing yourself as separate.