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For what it's worth, I understand that in some auto electrical systems removal of the battery, while the engine is running, will let the voltage rise to several times the expected 14 or so volts. I don't know if you plan to do that but thought I'd mention it, just in case.
If you follow the output of the alternator it should take you directly to a battery terminal. Connecting directly to the output of the alternator or the battery post is almost the same except for the small voltage drop that would exist. I am not sure what you plan to do so it's tough to comment.
When my son was busy with his automotive sound systems I had contemplated removing/rearranging the diodes from an alternator as part of a higher voltage power supply. I'd have installed two, possibly three batteries in series. Regardless of how you do it, alternators only put out so much.
Good luck. Whatever you end up doing be sure to provide appropriately sized fuses, fusible links or other overcurrent protection.