So... If you separate your Laboratory and the Guildhouse you got two strongholds but can only gain the benefits of one of them.
If you combine the two (technically you'd have to have built the larger guildhouse first before putting the smaller laboratory in it but I'd allow building the new stronghold as a larger expansion for the same cost) you'd get all the benefits of both strongholds BUT since this technically is a Guildhouse when you get the stat bonus you'd only get the wis (or cha) bonus.
RAW: "The only increase to an ability score you gain is from the first stronghold that grants this benefit.
Since the lab 6 is "the first stronghold that grants this benefit" you'd add 2 to Int (and raise the maximum Int by 2) and still keep the +1 Wis from the guildhouse.

To get both the lab benefits and the guildhouse benefits (sans ability bonus see above) you'd have to nestle the two building types within each other and effectively paying again for the smaller parts.

Quick calculation:
Step 1: Lab 2 = 1001(minumum grade 2)*2(luxurious) = 2002gp
Step 2: Guildhouse 3 = 5001(minimum grade 2)*2(luxirious - has to be the same as lab) = +10002
Step 3: Lab 5 = 50001(minimum grade 6)*2 = 100002 gp
For a total of: 112006gp

Meaning, you payed 12004gp more for the +1 Wis from the Guildhouse and a 15% discount on mundane goods and services.

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