So I went to deploy to test and for some reason kept getting access denied errors, but I'm global admin!! and Site collection admin!! What. It died on the code where I am uploading to the master page gallery. 

The problem was I had been deploying to /sites/site and not to the root web in other tests. The root web has a setting on it called DenyAddAndCustomizePagesStatus which is set to true but on the /sites/site sites, it's set to false :|. Even more annoying, I had also deployed to a demo tenant under the root web and this works, so I can only assume since it's a demo tenant with content that Microsofts code actually does this for you… https://support.office.com/en-us/article/Turn-scripting-capabilities-on-or-off-1f2c515f-5d7e-448a-9fd7-835da935584f?ui=en-US&rs=en-US&ad=US

Here's the code for deactivating on your site collection. Thanks to Ronny Lewandowski and SPMeta2 for helping me to solve this issue :). 

static void Main(string[] args)
{
            string siteUrl = ConfigurationManager.AppSettings["SiteUrl"];
            string adminUrl = ConfigurationManager.AppSettings["AdminUrl"];
            string userName = ConfigurationManager.AppSettings["AdministratorUserName"];
            string password = ConfigurationManager.AppSettings["AdministratorPassword"];
            var securePassword = new SecureString();
            foreach (var c in password) { securePassword.AppendChar(c); }

           Console.WriteLine("Start: Allow customisations...");
           DisableDenyAddAndCustomizePages(adminUrl, siteUrl, userName, securePassword);
            Console.WriteLine("End: Allow customisations... \n");
}

public static void DisableDenyAddAndCustomizePages(string adminUrl, string siteUrl, string userName, SecureString securePassword)
        {
            using (var ctx = new ClientContext(adminUrl))
            {
                ctx.Credentials = new SharePointOnlineCredentials(userName, securePassword);

                Tenant tenant = new Tenant(ctx);
                var siteProperties = tenant.GetSitePropertiesByUrl(siteUrl, true);
                ctx.Load(siteProperties);
                ctx.ExecuteQuery();

                siteProperties.DenyAddAndCustomizePages = DenyAddAndCustomizePagesStatus.Disabled;
                var result = siteProperties.Update();
                ctx.Load(result);
                ctx.ExecuteQuery();
                while (!result.IsComplete)
                {
                    Thread.Sleep(result.PollingInterval);
                    ctx.Load(result);
                    ctx.ExecuteQuery();
                }
            }
 }

ALSO, here is the code in PowerShell if you just want to quickly run it once:

Clear-Host
$spOnlineUser = ''
$spOnlinePassword = ''
$spOnlineSiteAdminUrl = ''
$spOnlineSiteUrl = ''
 
$cred = New-Object -TypeName System.Management.Automation.PSCredential -argumentlist $spOnlineUser, $(convertto-securestring $spOnlinePassword -asplaintext -force)
Connect-SPOService -Url $spOnlineSiteAdminUrl -Credential $cred
Write-Host "Connecting to " $spOnlineSiteUrl
 
$site = Get-SPOSite -Identity $spOnlineSiteUrl
Write-Host "Connection Successful!!" -ForegroundColor "Green"

Set-SPOSite -Identity $spOnlineSiteUrl -DenyAddAndCustomizePages 0

Write-Host "Finished!!" -ForegroundColor "Green"