As usual, I will answer myself.

It seems the issue was a URL rewrite rule that I had for adding trailing backslash.

I just added the following line to the rewrite rule:

<add input="{URL}" pattern="\.axd$" negate="true" />

so the full rule is:

 <rule name="Add trailing slash" enabled="true" stopProcessing="true">
      <match url="(.*[^/])$" />
      <conditions>
        <add input="{HTTP_URL}" pattern="^.*/(ucommerce.*|payment-page.*|login-wizard|customer-success|umbraco|umbraco_client|client|install|api|App_Plugins)" negate="true" />
        <add input="{URL}" pattern="\.axd$" negate="true" />
        <add input="{HTTP_HOST}" pattern="localhost" negate="true" />
        <add input="{REQUEST_FILENAME}" matchType="IsFile" negate="true" />
        <add input="{REQUEST_FILENAME}" matchType="IsDirectory" negate="true" />
        <add input="{REQUEST_FILENAME}" pattern="(.*?)\.xml" negate="true" />
      </conditions>
      <action type="Redirect" redirectType="Permanent" url="{R:1}/" />
    </rule>

That stopped the redirect for the webResource.axd and scriptResource.axdm, and solved the issue, as the original problem was that both of this files return 404.

Cheers