The short answer is that you may employ the simple past perfect to express a continuing action only when the expression is atelic or bears in context a reasonably natural atelic interpretation.
A telic expression is one which has a goal or ending point "built in" to its sense—finish, for instance. Employing the test suggested in the article linked above, it makes perfect sense to say He finished in an hour, but not (normally) He finished for an hour.
Expressions which do not have such a goal are atelic. In your first example, work is an atelic expression: using the same test, He worked for an hour is acceptable, but not (normally) He worked in an hour. Atelic expressions are, so to speak, inherently continuous. Consequently, a simple past perfect construction use supports a continuous sense; this is why the two are "interchangeable".
Your other examples, however, are telic. Eating dinner and cleaning a room are not (normally) protracted indefinitely, they come to an end when the dinner is consumed and the room is clean. Consequently, using simple perfect constructions implies completion, and if you want to convey that the action continues you must employ a progressive construction.
Note, however, that "telicity" is a very subtle matter in practice. As the linked article tells you, grammarians are in some disagreement over just how it works; and I have been careful to qualify all my analyses with the (normally) tag.
Note, too, that there is an alternative to the two constructions you illustrate. The past progressive ("I was eating dinner when ... " and "I was cleaning my space when ... ") is more natural to my ear than the past perfect progressive. You want the past perfect progressive only if you employ a qualifier like since dawn, which removes the focus from the present-in-the-past to the past-in-the-past, the stretch of time which preceded the present-in-the-past.
If the present passive is used with a resultative verb, then the focus is on the present state. Conversely, if the perfect passive is used, there is a greater emphasis on the action that caused the present state. So in the following examples of housework, the present passive places the focus on the resultative state:
The car is washed.
The furniture is waxed.
The shoes are polished.
The clothes are ironed.
The beds are made.
The table is laid.
The perfect passive, in contrast, places greater emphasis on the action:
The car has been washed.
The furniture has been waxed.
The shoes have been polished.
The clothes have been ironed.
The beds have been made.
The table has been laid.
Best Answer
These versions seem normal to me (native English speaker):
He must have been sitting there for two hours already
He must already have been sitting there for two hours
or:
He must have been sitting there for two hours by now
The position of "already " is important to sound idiomatic. The version in the question sounds "wrong " to me mainly for this reason, not because of the verb forms used.