How to add a pane (view content pane) to an existing panel page via a Feature module or programmatically?
This looks like the start of what can lead into you what I call "Features Hell". :)

It's possible to make features more maintainable and minimize conflicts if you organize them by small groups or single feature components. Here's what I mean:


You have content types X and Y
You have, I assume, panelizers for content type X and Y
You have views with content pane displays that you want to add to a
panelizer


This can be done by divided up your features into four different modules.

foobar_field_bases: contains the fields from content type X and Y under the "Field Bases" component. This stores the global settings of the fields.

foobar_content_types: contains content types X and Y from the features Content Types component, and the content type fields under the Field Instances component.

foobar_views: contains all your views

foobar_panels: contains all panel-related components such as panel layouts, panel renderers, panelizers, page managers.

It may seem like that's harder to maintain because you have more modules now, but consider your issue. You want to update the panelizer content with a view content pane. All you do is make sure the view is in foobar_views. If not, recreate foobar_views with your new view. If it is, update the foobar_views feature so it contains the new display in the feature module. Then do a feature update on foobar_panels.