When all you indexes have included all the other columns, do you still have the penalty for a wide clustered index? So I hear sometimes that I should not use a clustered index on a wide column, mainly because it is being referenced in all other indexes. 

When all my other indexes on this table include all other columns - is there still this (extra) penalty?

(This table has no external references on the clustered index by other tables)

For reference my table looks a bit like this:

PartOfNaturalKey1    int
PartOfNaturalKey2    varchar(10)
PartOfNaturalKey3    varchar(20)
PartOfNaturalKey4    int
Value                varchar(10)
LastChanged          datetime2(7)
Invalid              bit


The Natural Key is unique and will (almost never) change.
If you have in every index all columns and you have a PK , and another 2 indexes , one on Value and one on LastChanged , you really multiplied the table by 4. This will make the table really slow for all operations. 

Add an ID column , make it PK  and build indexes as you need based on the statements that run on the table. 

Don't create an index on Invalid, it's a bit column , it's usually not useful . 

Try to keep a rule that all indexes should be smaller in size than the table.