Adal.js and Azure AD secured web API - Access SharePoint with user context

On further inspection we have noticed that the request was throwing an error

{x-ms-diagnostics: 3000003;reason="Invalid audience Uri 'Audience URI as specified in webApiAppIdUri'.";category="invalid_client"
SPRequestGuid: 32439d9d-408d-3000-2140-22c0c88730a5
request-id: 32439d9d-408d-3000-2140-22c0c88730a5
Strict-Transport-Security: max-age=31536000
X-FRAME-OPTIONS: SAMEORIGIN
SPRequestDuration: 12
SPIisLatency: 2
MicrosoftSharePointTeamServices: 16.0.0.5611
X-Content-Type-Options: nosniff
X-MS-InvokeApp: 1; RequireReadOnly
Date: DATE IN GMT
P3P: CP="ALL IND DSP COR ADM CONo CUR CUSo IVAo IVDo PSA PSD TAI TELo OUR SAMo CNT COM INT NAV ONL PHY PRE PUR UNI"
Server: Microsoft-IIS/8.5
WWW-Authenticate: Bearer realm="TENANT GUID",client_id="00000003-0000-0ff1-ce00-000000000000",trusted_issuers="00000001-0000-0000-c000-000000000000@*,https://sts.windows.net/*/,00000003-0000-0ff1-ce00-000000000000@90140122-8516-11e1-8eff-49304924019b",authorization_uri="https://login.windows.net/common/oauth2/authorize"
X-Powered-By: ASP.NET
}

We have given the native app and the web app permissions to all SharePoint sites.

We have defined the endpoints object in the ADAL.js config as follows:

var endpoints = {};
this.adalEndPoints[_spPageContextInfo.siteAbsoluteUrl + "/_api/web/lists"] = _spPageContextInfo.siteAbsoluteUrl + "/_api/web/lists"; // here we have tried different permutations
...
// ADAL endpoints for automatic hooking
endpoints: 

And here is a simple C# web client for testing purposes we have made:

string result = String.Empty;
            string requestUri = OfficeDevPnP.Core.Utilities.UrlUtility.Combine(siteCollectionUrl, "_api/web/lists");
            try
            {
                using (var httpClient = new HttpClient())
                {
                    httpClient.BaseAddress = new Uri(siteCollectionUrl);
                    httpClient.DefaultRequestHeaders.Accept.Clear();
                    httpClient.DefaultRequestHeaders.Accept.Add(new System.Net.Http.Headers.MediaTypeWithQualityHeaderValue("application/json"));
                    httpClient.DefaultRequestHeaders.Authorization = new System.Net.Http.Headers.AuthenticationHeaderValue("Bearer", authToken);

                    var request = httpClient.GetAsync(requestUri).Result;
                    request.EnsureSuccessStatusCode();
                    if (request.StatusCode == System.Net.HttpStatusCode.OK)
                    {
                        result = request.Content.ReadAsStringAsync().Result;
                    }
                }
            }
            catch(Exception ex)
            {

            }

            return result;

Anybody could point me to a solution?