The question would be do you actually need those 2 junction type tables?
If you have 2 'identity' type items in 2 different tables and you want to relate the 2 together in multiple different combinations (ie. 1 or more farms associates to more than 1 record in the other table and you can have many different combinations), you can use the junction type tables as your last diagram shows. This allows you more flexibility whereby you can again, join 1 farm to multiple other items in the other table (or vice-versa if looking at it from the other table's perspective). If though, you only need to join 1 item from the other table to 1 specific farm (or vice-versa) (and won't need to join that specific farm to another item in the other table....or join the other item in the other table to multiple farms), I'd then go the route of just adding the ID from the other table to your farm table or just add the farmID to your other table.
When you look at the 2 relational tables, you need to decide if you need to make multiple different combinations between the 2 id records from the 2 tables. If so, then use the junction type table. If only 1 record in 1 table assoicates to a record in the other table or vice-versa (ie. 1 to 1 or 1 to many versus many to many), then look at adding your ID field to either one of the tables.
For example:
Ex:
Many different Farms and many different 'contacts' for any specific farm and 1 farm can have many contacts or a specific contact can be assoicated to many different farms (along with other contacts to the same farm) - I'd use a junction type table.
Ex:
1 Farm only ever has 1 contact or 1 contact is tied to only 1 specific farm (or tied to many farms but no other contacts to those farms) - I'd just put the ContactID in the Farm table or FarmID in the Contacts table.
I hope that helps.