You can use all Sitecore types to access and manipulate field value.
Example
# get your ph settings item
$phSettings = gi -path '/sitecore/layout/Placeholder Settings/content'
# read field and assign it to MultilistField type
[Sitecore.Data.Fields.MultilistField]$field = $phSettings.Fields["Allowed Controls"]
Now you can read and set values
# read IDs from an array of IDs
$field[0]
# replace ID inside an array
$phSettings.Editing.BeginEdit()
$field.Replace("{493B3A83-0FA7-4484-8FC9-4680991CF742}","{493B3A83-0FA7-4484-8FC9-4680991CF743}")
$phSettings.Editing.EndEdit()
MultilistField
is an extension of Sitecore.Data.Fields.DelimitedField
field type. Decompile it and see other methods available:
public int Count
public string[] Items
public bool Contains(string item)
public string Add(string item)
public string Remove(string item)
public int IndexOf(string item)