SOQL Lib 6.1 toMap optimisations are incompatible with InnerJoin queries

[packocz]

Describe the bug
A clear and concise description of what the bug is.

To Reproduce
Query to find Permission Sets which contain a CustomPermission working in v5, breaks with v6.1. The last "AND ParentId != NULL" filter is added by the optimisation and is the culprit in this case.

SELECT Id FROM SetupEntityAccess WHERE (SetupEntityId IN (SELECT Id FROM CustomPermission WHERE (DeveloperName IN ('CustomPermissionName'))) AND Parent.IsOwnedByProfile = FALSE) AND ParentId != null

SOQL.of(SetupEntityAccess.SObjectType)
			.whereAre(
				SOQL.FilterGroup
					.add(
						SOQL.Filter.with(SetupEntityAccess.SetupEntityId)
							.isIn(
								SOQL.InnerJoin.of(CustomPermission.SObjectType)
									.with(CustomPermission.Id)
									.whereAre(
										SOQL.FilterGroup.add(SOQL.Filter.with(CustomPermission.DeveloperName).isIn(customPermissions))
									)
							)
					)
					.add(SOQL.Filter.with('Parent', PermissionSet.IsOwnedByProfile).isFalse()) 
			)
			.systemMode()
			.withoutSharing()
			.mockId(MOCK_ID_GET_PERM_SETS)
			.toMap(SetupEntityAccess.ParentId);

Expected behavior
Query should work, in some scenarios the key field used simply cannot be null. We should have an option to not "optimise". At least let's document a suitable workaround for these situations (not sure what it is yet - we are using toList for now and mapping in apex).

[pgajek2]

System.QueryException: Semi join sub-selects are only allowed at the top level WHERE expressions and not in nested WHERE expressions.

[packocz]

System.QueryException: Semi join sub-selects are only allowed at the top level WHERE expressions and not in nested WHERE expressions.

Yes that's the error. It did not happen with the same query in previous versions. The auto-added conditions ParentId!=NULL is what causes it.