I use SlowCheetah to convert my web.config to production. I initially tried what you tried, but found that I had to add an empty
<rewrite>
<rules />
</rewrite>
to web.config database
and then write a transformation like
<system.webServer>
<rewrite>
<rules>
<rule name="Redirect to HTTPS" stopProcessing="true" xdt:Transform="Insert">
<match url="(.*)" />
<conditions>
<add input="{HTTPS}" pattern="^OFF$" />
</conditions>
<action type="Redirect" url="https://{HTTP_HOST}/{R:1}" redirectType="Permanent" />
</rule>
</rules>
</rewrite>
</system.webServer>
(this is a forwarding conversion, but I think the same principle should apply).
Note xdt:Transform="Insert"to insert a new node into the skeletal <rules />in the base configuration file.