How to bond both ends of raceway containing grounding electrode conductors?

Your problem: neither the Code nor electrical-fitting-makers ever envisioned someone stuffing two grounding electrode conductors down the same ferrous conduit

You are correct that using ferrous conduit and conduit bodies here would require you to conform with NEC 250.64(E):

(E) Raceways and Enclosures for Grounding Electrode Conductors.

(1) General. Ferrous metal raceways and enclosures for grounding electrode conductors shall be electrically continuous from the point of attachment to cabinets or equipment to the grounding electrode and shall be securely fastened to the ground clamp or fitting. Ferrous metal raceways and enclosures shall be bonded at each end of the raceway or enclosure to the grounding electrode or grounding electrode conductor to create an electrically parallel path. Nonferrous metal raceways and enclosures shall not be required to be electrically continuous.

(2) Methods. Bonding shall be in compliance with 250.92(B) and ensured by one of the methods in 250.92(B)(2) through (B)(4).

(3) Size. The bonding jumper for a grounding electrode conductor raceway or cable armor shall be the same size as, or larger than, the enclosed grounding electrode conductor.

(4) Wiring Methods. If a raceway is used as protection for a grounding electrode conductor, the installation shall comply with the requirements of the appropriate raceway article.

However, the NEC doesn't speak here to what to do in your situation where you have two grounding electrode conductors in the same piece of ferrous conduit. Normally, for a single GEC in a conduit, you can use a lug-equipped grounding/bonding locknut (Bridgeport 162-G or equivalent for 3/4") on the box entrances and a grounding hub fitting (Bridgeport MCH-075) or a hub clamp (Bridgeport 1325-B or equivalent) on the grounding electrode end of the conduit. However, all of the aforementioned fittings are only rated to accept a single wire, and you have two wires. As a result of that, we'll need to find an alternative approach.

Jumpering and tapping our way to success

The good news, though, is we still can use grounding/bonding locknuts with lugs to accomplish the job of bonding the enclosure knockouts as before; however, we need to jumper from said lugs to the grounding electrode conductor itself, not to a grounding or neutral bar in the enclosure. This will require 6 AWG copper (or whatever size your existing GECs are) for the jumper, as well as 6AWG to 6AWG lay-in parallel mechanical taps (Ilsco GTA-2-2 or equivalent) to connect each end of the jumper to a GEC, in addition to the aforementioned grounding/bonding locknuts (which come in various sizes, just make sure to get ones that have lay-in lugs on them). In this situation, the bonding jumper extends from one tap connector, through the lay-in lug on the grounding/bonding locknut, then to the other tap connector on the other grounding electrode conductor, thus connecting both GECs to the raceway bonding point.

At the exit points, though, we'll need to take a somewhat different approach. The aformentioned tap connectors are dual-rated Al9Cu, so using them near the ground is a bad idea for corrosion reasons, and there aren't any equivalent direct burial products out there. So, I'd use an extra grounding clamp on each ground rod, with a jumper from one extra rod grounding clamp, through a lay-in pipe grounding clamp rated for direct burial (T&B JDLI or equivalent) that is fitted on the conduit to bond it, and on to the other extra rod grounding clamp. This works because 250.64(E)(1) lets us land these bonding jumpers directly on grounding electrodes at the grounding-electrode end of the raceway, instead of landing them on GECs.