Will a tour of the necropolis below St Peters be included?
Will the Capuchin monastery on via Veneto be included?
No and no.
But it does end under St. Peter’s basilica and you can visit the tombs of former popes and smaller chapels. It is not part of the tour, you are on your own. You can then go into the basilica.
Scavl Tour is the Necropolis beneath St Peters Basilica. If you search St Peter's Necropolis it takes you to the Vatican Scavi Tour site to book it. The Body/Bones of St Peter's are buried there.
Tickets are very limited and hard to come by, you have to request months in advance then approximately 30 days before your requested date you will get yes or no notification.
The tour ends in the grottoes under the church and you can come back up to St Peters to see the church and walk through the Holy Doors if you want to.
Normally, you are able to go into St. Peters after the Scavi tour.....BUT, there is no guarantee. If you are there during certain celebrations or private events (such as when the beatification of Pope Paul (I think it was) took place....no entry into the St. Peters was allowed afterward. There may be certain other private masses that MIGHT exclude entry, too.
You are probably asking about the tour of the burial area below the basilica called the Necropolis, and has also been referenced as the Scavi, which generally just means an excavation. This is what you're asking about, right?
https://www.basilicasanpietro.va/en/products/the-necropolis
So yes, as people posted above, it's a tour deep below the basilica. No, it doesn't include the Capuchin Crypt as that's an unrelated, much less ancient 'bone chapel' in a different part of town.
There is another necropolis - Necropolis of the Via Triumphalis - that the Vatican conducts tours of but only a couple days a week and is unlikely to be the one you're asking about. It has caused some confusion in the past though so just to be on the safe side...
https://tickets.museivaticani.va/home/fromtag/1/1748581200000/VG-Triumphalis
https://www.museivaticani.va/content/museivaticani/en/collezioni/aree-archeologiche0/necropoli-della-via-triumphalis/necropoli-della-via-triumphalis.html