Grand staff distance excludes tablature and organ pedal staff
Grand staff distance works for Piano, but not for the 3 staves of an Organ (it only considers the top 2 staves to belong to the grans staff) and not to any instrument that gets a staff added.
This affects for example also Guitar, normal plus tablature staves, linked or not, which in 2.x were treated as grand staves. but also any other instrument where a staff gets added, irrespective of staff type or whether linked or not.
Additional issue: in 2.x the 3 staff organ have the barlines connecting all 3 staves, on 3.0 these are only connecting the top staves, not sure whether this is intentional