Actually no, they do not outrank the Chapter Masters of the Adeptus Astartes or anything else in that list really. The Holy Ordos were founded by Malcador the Sigilite to police and oversee the Imperial Adeptus. They do not however have purview over their actions unless they may prove that those are opposed to the Imperium.
The figures you mentioned cannot be ordered save from the Emperor himself, that and the High Lords that act as his voice. An Inquisitor has great power yes, but even that has limits. Go pissing off a Lord Admiral or a Sector Governor and you can find yourself isolated from your peers. Piss off a Chapter Master or a High Fabricator and you can find yourself dead.
Depends. Space Marine chapters are set aside from the rest of the Imperium but the Emperor set up the Inqusition to be his left hand and in the backgound it mentions that Inquisitors are...
'the only individual that is exempt from its scrutiny is the Emperor himself. If he has good cause, an Inquisitor may demand any service from any Imperial citizen, up to and including the High Lords of Terra. The Adeptus Custodes who guard the Emperor's palace and person are exempt from conscription, because their duty to the Emperor is clear and unchanging'
As to the Space Marines...
'When it comes to the Adeptus Astartes, Inquisitors often show some discretion, as Space Marine Chapters are often willing to come to blood over any infringement on their Emperor-granted autonomy. However, not even the Adeptus Astartes are immune from the Inquisition's scrutiny and justice, and entire worlds have been destroyed in order to cleanse them if they were deemed traitorous.'
Edited by Kahadras