hmmm mixed bag of tricks, at least to the untrained eye. Every attempt was done after loading the same save.
Attempt #1
As soon as I choose the layout suddenly both plot #2 and #3 see some scaffolding action. Plot #2 becomes a shed. Plot #3 becomes 'un-constructed'(is that even a word?). I no longer get the duplicate warning but still get the 'placeholder' message.
Attempt #2
I choose the layout, plot #2 doesn't care, remains unfazed, 'I am a placeholder and that is that.' Plot #3 looks at plot #2 and goes 'well, if you ain't changing neither am I': I get the scaffolding animation but the plot remains unbuilt so now the plaque in both plots just reads 'Scavver Support' but I no longer get the duplicate message. Still get the placeholder message.
Attempt #3
Choose the layout, plot #2 gives zero f**ks. Plot #3 kind of does but doesn't. I get the scaffolding animation, plot remains unbuilt. Before I can exit and reload I get the scaffolding again and now becomes a shed. No duplicate message but yes to placeholder message.
Attempt #4
Before doing anything I fast travel around three settlements. Go back to Tenpines, do the deed... Plot #2 once more unchanged, plot #3 scaffolding comes and goes, nothing happens, plaques on #2 and #3 still read 'Scavver Support`
Do some more fast travelling, come back to Tenpines, now I get a 'Duplicate Sorter' message. Plots remain unchanged.
Attempt #5
F**k I have to go to work!
EDIT: Full disclosure, my papyrus log is rammed with some kind of NukaWorld related script error. Something about not being able to set the state of a protectron pod?
After that there is another battering round of something I think might be related to one of JtBryant's mods. I have messaged him in the nexus about it:
[None].JtB
arracksFactionSupport.CheckQuestTriggers() - "C:\Users\tnboy\AppData\Local\Temp\PapyrusTemp\JtB\BarracksFactionSupport.psc" Line 57
[None].JtB
arracksFactionSupport.::remote_Actor_OnPlayerLoadGame() - "C:\Users\tnboy\AppData\Local\Temp\PapyrusTemp\JtB\BarracksFactionSupport.psc" Line 139
[08/09/2017 - 07:11:21PM] error: Cannot access a variable of a None struct
I don't know if either of those could be related to this issue.
EDIT2: I think there might be room for confusion in my prose. In neither attempt I touched plot #2 at all, I just did as instructed: select plot #3, let it go kablam then manually choose the relevant blueprint through the ASAM menu.