Taking the covenants in turn
2) Yes, they are usually the subject of enquiries before contract but it is not at all unusual for maintenance of boundaries to be recorded as covenants on title. Sometimes the result of a previous dispute or simply because neighbours wish to record who is responsible to prevent future disputes. But as I say, it is not unusual for this be recorded.
3) I completely agree with your comments here, if this boundary is nothing to do with the seller, they are not entitled to insist on a covenant to be created. If the seller is not the owner of the land which would have the benefit of the covenant, he cannot create it. I would query this with their solicitor.
In respect of Churston - it is essentially both as they work hand in hand. It was held the covenant did not run with the land, thus the dominant proprietor cannot claim and the servient proprietor was under no obligation.
I would most certainly revert to the seller's solicitor and query the third covenant as the proprietor of No.7 (as referred to in the transfer) is not a party to the transfer therefore this covenant cannot be created.
I would expect the solicitor to insist on the other two points so it may be worth suggesting that you are happy to enter into a separate agreement in this regard or have the wording amended so it is personal rather than binding on the land.
I hope this helps.