You would cast a 4th-level Ray of Enfeeblement, and it would cost a 9th-level spell slot.

Without Heighten Spell, it would be a 1st-level Ray of Enfeeblement costing a 6th-level spell slot.

Metamagic does not increase the effective level of a spell. Instead, for powering up the spell with other effects (like chain and empowerment), you pay the price of a higher-level spell slot for a lower-level spell. If you wind up with a 1st-level spell taking up a 6th-level spell slot thanks to metamagic, it's still a 1st-level spell.

Powering up the effective level of a spell is exclusively the role of Heighten Spell. Think about it: if Chain Spell meant you were also casting an effective-level-4 Ray of Enfeeblement, what would be the point of Heighten Spell even existing?

See the bolded text here, in which it increase the effective level of a spell - emphatically, unlike other metamagic feats:

Heighten Spell [Metamagic]

Benefit: A heightened spell has a higher spell level than normal (up to a maximum of 9th level). Unlike other metamagic feats, Heighten Spell actually increases the effective level of the spell that it modifies. All effects dependent on spell level (such as saving throw DCs and ability to penetrate a lesser globe of invulnerability) are calculated according to the heightened level. The heightened spell is as difficult to prepare and cast as a spell of its effective level.

The feat Tenebrous Spell improves shadow spells according to your initial assumption

That's because, according to Metamagic Feats, Effects of Metamagic Feats on a Spell says that

In all ways, a metamagic spell operates at its original spell level, even though it is prepared and cast using a higher-level spell slot. Saving throw modifications are not changed unless stated otherwise in the feat description.

So the feat's benefits don't also increase the spell's actual level (hence the saving throw DC) because the feat doesn't say that happens, but the feat's benefit increases the save DC independent of the metamagic spell's new level if conditions are met.

Ignoring this rule makes metamagic feats in general more powerful. That is, if all metamagic feats increase the spell's actual spell level instead of merely increasing the spell slot the spell occupies, modifying a spell with, for example, the feat Quicken Spell, in addition to changing the spell's casting time, would have the glorious side effect of also increasing the spell's saving throw DC by +4. And, of course, under such rules, most wouldn't bother anymore with the feat Heighten Spell, which is the feat that for-reals changes the spell's level, usually to keep low-levels spells relevant by increasing their saving throw DCs.