The FG1 was purchased by the RN for fleet defence, so when Eagle was decommissioned in the late 1960s, it made sense to base the 20 available airframes at Leuchars with 43 Sqn as a SACLANT assigned squadron for fleet defence. Whilst the fit might seem poor by modern standards, it was far superior that of the Lightnings it replaced. Similarly when Ark Royal was decommissioned it made sense to allocate her FG1s to 111 Sqn in the same role and spread the released FGR2s amongst the more numerous other southern and RAFG squadrons where the fit, including special weapons wiring, was designed for the ground attack role until they all transferred over to AD.
The simulator story is more complicated.