JWT CSOM/REST Azure Active Directory

We have been trying to make requests to sharepoint using CSOM/REST Authentication Bearer header requests with a token. It is related to this question below:

C# CSOM Sharepoint Bearer request from azure active directory

There is only one link/example that works all others including the android ADAL approach don't work.

https://samlman.wordpress.com/2015/02/27/using-adal-access-tokens-with-o365-rest-apis-and-csom/

They don't seem to return as long a token, when we look at the token in JWT parser, we can see that the scp value is different, the one that fails has user_impersonate, but the working one has AllSites.Manage AllSites.Read AllSites.Write MyFiles.Read MyFiles.Write. The aud url is also different, are one or both of these the problem and how do I get it working?

This is the ones that fails:

{
  "aud": "https://srmukdev.onmicrosoft.com/3Squared-Api-Test",
  "iss": "...",
  "iat": ...,
  "nbf": ...,
  "exp": ..,
  "acr": "...",
  "aio": "...",
  "amr": [
    "pwd",
    "mfa"
  ],
  "appid": "...",
  "appidacr": "0",
  "e_exp": ...,
  "family_name": "...",
  "given_name": "...",
  "ipaddr": "...",
  "name": "...",
  "oid": "...",
  "onprem_sid": "...",
  "platf": "3",
  "scp": "user_impersonation",
  "sub": "...",
  "tid": "...",
  "unique_name": "...",
  "upn": "...",
  "ver": "1.0"
}

This is the ones that works:

{
  "aud": "https://srmukdev.sharepoint.com/",
  "iss": "...",
  "iat": ...,
  "nbf": ...,
  "exp": ...,
  "acr": "...",
  "aio": "...",
  "amr": [
    "pwd",
    "mfa"
  ],
  "app_displayname": "...",
  "appid": "...",
  "appidacr": "0",
  "e_exp": ...,
  "family_name": "...",
  "given_name": "...",
  "ipaddr": "...",
  "name": "...",
  "oid": "...",
  "onprem_sid": "...",
  "platf": "3",
  "puid": "...",
  "scp": "AllSites.Manage AllSites.Read AllSites.Write MyFiles.Read MyFiles.Write",
  "sub": "...",
  "tid": "...",
  "unique_name": "...",
  "upn": "...",
  "ver": "1.0"
}