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Given a recent patch where an underground location will work, so I have two locations for alt-main bases when starting a game.
Highly - Recommended below ground: The Forgotten Vault Settlement Into Darkness https://www.nexusmods.com/fallout4/mods/42297 I feel the below-ground gives the player some serious advantages in performance and stability. This particular below ground settlement has immersive advantages of several access points to above-ground locations. Also, a SS author so you know the workshop is correctly set-up.
Highly - Recommended above ground and an alternative to Sanctuary. Settlements Redone - Lakeside Cabin Settlement by Tarsis31 and Yagisan https://www.nexusmods.com/fallout4/mods/35553 Also, a SS author so you know the workshop is correctly set-up.
As a mid-game locations here are two others I love!
by Pra and Neeher