Those bolts should be that way. Its not a problem with manufacturing. The bolts are for the 1985 California model that has an extra heat shield that goes on the back of the alternator. This is the superseded part and is currently the only one that's available from the ORIGINAL supplier. Alternators from other suppliers that have the flush length bolts are either old stock or are of their own casting & manufacturing (non-oem).

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1985 300TD - "Panzer Wagen" - undergoing full restoration (resto - mod)
2014 GLK250 Bluetec - Wife's car

Mercedes-Benz Master Certified Technician.

http://www.flickr.com/photos/joshuajeeper/

I'd return it based on this pic alone. The regulator is a cheap, non Bosch unit.
How do I know? An alternator rebuild place gave me one for nothing and it does not look well made. Very different design than Bosch, with parts potted in Epoxy. I'd return it for one with a Bosch regulator.

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85 300D turbo pristine w 157k when purchased 167,870 July 2025
83 300 D turbo 297K runs great. SOLD!
83 240D 4 spd manual- parted out then junked

Took your advice and returned the alternator to NAPA. I sourced a genuine Bosch 65 amp unit which should arrive in a few days. Since this experience, I am planning on obtaining an extra alternator and extra starter for both cars. Sure, they'll sit on the shelf but if either goes out on the car, I can simply grab one off the shelf and install......minimum down time.

The brushes on the regulator is the only part that wears. The electronic components do not wear out. Actually, they have been "burned in" and are less likely to fail than a new one.

The brushes on the Bosch regulators cannot be un-soldered with a regular iron and has to be drilled out, then the new brushes can be soldered on. Bosch use a very high temperature "solder". This is a tip from the alternator rebuild place that gave me the cheapo regulator.

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85 300D turbo pristine w 157k when purchased 167,870 July 2025
83 300 D turbo 297K runs great. SOLD!
83 240D 4 spd manual- parted out then junked

My thought. But, on my 85 CA 300D, the bolts aren't that long, w/ maybe just 4 threads for the hex nuts that screw on to stand-off the heat shield, so might be a kludge to the standard alternator bolts. I would think if you cut them shorter, NAPA wouldn't notice or care when returned. The main reason for cutting is so you can better swing a wrench when installing/adjusting. The CA heat shield makes that task more challenging.

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1984 & 1985 CA 300D's
1964 & 65 Mopar's - Valiant, Dart, Newport
1996 & 2002 Chrysler minivans