I guess now it's possible. If you insert VersionOverrides in the manifest file an leave it empty, then the outlook client will not show the app but the outlook on the web client will show the app.
Example:
<VersionOverrides xmlns="http://schemas.microsoft.com/office/mailappversionoverrides" xsi:type="VersionOverridesV1_0">
<Requirements>
<bt:Sets DefaultMinVersion="1.3">
<bt:Set Name="Mailbox" />
</bt:Sets>
</Requirements>
<Hosts>
<Host xsi:type="MailHost">
<DesktopFormFactor>
<FunctionFile resid="functionFile" />
<ExtensionPoint xsi:type="MessageReadCommandSurface">
</ExtensionPoint>
</DesktopFormFactor>
</Host>
</Hosts>
Don't forget the namespace:
xmlns:bt="http://schemas.microsoft.com/office/officeappbasictypes/1.0"
xmlns:mailappor="http://schemas.microsoft.com/office/mailappversionoverrides"