You have to update/inherit all mail templates that are required (Settings > Companies > Email Templates > Review All Templates). In addition, Odoo uses two base templates (mail.mail_notification_layout and mail.mail_notification_light in the mail_templates.xml from the mail module). Update/inherit these as well. E.g.,

Regarding the changes. You should replace the following:
<img t-att-src="'/logo.png?company=%s' % (company.id or 0)" style="padding: 0px; margin: 0px; height: auto; max-width: 200px; max-height: 36px;" t-att-alt="'%s' % company.name"/>
With this:
<t t-if="company.logo">
<img t-att-src="image_data_uri(company.logo)" style="padding: 0px; margin: 0px; height: auto; max-width: 200px; max-height: 36px;" t-att-alt="'%s' % company.name"/>
</t>
<t t-else="">
<h3 style="padding: 0px; margin: 0px; height: auto; max-width: 200px; max-height: 36px;" t-field="company.report_header"/>
</t>
This will use the logo set for the company. So if you change this, the logo get's updated for the emails as well.
I hope this helps!