I have no concrete proof, but would presume 'yes', particularly to keep up/stay ahead of Sky Q. Virgin have full control over the Horizon software, so presume it will improve over time. For example, Sky recently introduced the 'What Can I Watch' voice feature to show personalised recommendations. Their voice search has improved dramatically since launch.
Which search are you using, if you go to Catch Up you can select iPlayer at the top and it will list all series / programmes currently available on iPlayer, also if you do a search for Eastenders, which I don't watch, the earliest episode available on iPlayer from the all episodes list is the 30 March, you could always use the iPlayer app which seems to go back further. If it was a BBC specific programme I would use iPlayer app, you may just be doing a general search for a film for example that isn't still available on iPlayer so that's why you don't get results for iPlayer. Do you have any specific examples of programmes that don't show in search results for iPlayer to be able provide a clearer answer.
I would like to see all available programs to me, when I use the search and not be shown programs I have to pay for.
A point that's come up on here over the years. The EPG also shows all channels available, regardless of whether you subscribe to them or not.
The answer is that between the broadcasters & the platform providers, they see this is a "shop window" which is a polite way of describing marketing.
The STB software doesn't allow for differentiation of what's displayed, based on your package - and this is never likely to happen. It would also add more complication and possibly induce the possibility of errors in the search results.
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