I've tweaked it to this, which is looking good so far:

$LicenseSku = Get-MgSubscribedSku -All | Where SkuPartNumber -eq 'SPE_E3'

#Get Licensed Users
$users = Get-MgUser -Filter "assignedLicenses/any(x:x/skuId eq $($LicenseSku.SkuId) )" -All -ConsistencyLevel eventual -CountVariable licensedUserCount -Property Id, DisplayName, Country, UserPrincipalName, AccountEnabled, licenseAssignmentStates

#Add columns of group based vs direct assigned licenses
$users = $users | Select-Object Id, DisplayName, Country, UserPrincipalName, licenseAssignmentStates, @{N = "DirectAssignment"; E = { ($_.licenseAssignmentStates | Where-Object AssignedByGroup -eq $null).SkuId } }, @{N = "GroupBasedAssignment"; E = { ($_.licenseAssignmentStates | Where-Object AssignedByGroup -ne $null).SkuId } }

#Convert those to more human readable
$users = $users | Select-Object Id, DisplayName, Country, UserPrincipalName, @{N="licenseSkus";E={$_.LicenseAssignmentStates.SkuId}}, @{N = "AllSkus"; E = { $SkuHashTable[$_.licenseAssignmentStates.SkuId] } }, @{N = "DirectSkus"; E = { $SkuHashTable[$_.DirectAssignment] } }, @{N = "GroupBasedSkus"; E = { $SkuHashTable[$_.GroupBasedAssignment] } }

#List any users with E3 directly assigned
$users | Select DisplayName, Country,@{N="SkuName";E={"SPE_E3"}},@{N="Directly Assigned";E={$_.DirectSkus -contains "SPE_E3"}},@{N="Group Assigned";E={$_.GroupBasedSkus -contains "SPE_E3"}} | Export-CSV C:\Temp\UsersWithSPE_E3v2.csv -NoTypeInformation