I think the design is crap and causes more trouble than its worth.
I am only guessing but i think they must have been trying to comply with a mining spec where the machine has total electrical isolation in the off state.
Use a reasonable sized wire if you are going to bypass the relay as you have described.
The only issue which needs to be checked and or dealt with is how the alternator is started.
In a motor car the alternator warning light on the dash is used to excite the alternator when the motor starts.
On your machine they use a resister between the alternator B+ terminal and the field winding.
this circuit was energized when the ignition closed the battery relay.
It might be that being bypassed the field circuit of the alt is draining your battery's in the off state.
You will have to remove a battery terminal when not running and check with a meter that is not happening.
If it is the wiring can be fudged but check first.
I am only guessing but i think they must have been trying to comply with a mining spec where the machine has total electrical isolation in the off state.
Use a reasonable sized wire if you are going to bypass the relay as you have described.
The only issue which needs to be checked and or dealt with is how the alternator is started.
In a motor car the alternator warning light on the dash is used to excite the alternator when the motor starts.
On your machine they use a resister between the alternator B+ terminal and the field winding.
this circuit was energized when the ignition closed the battery relay.
It might be that being bypassed the field circuit of the alt is draining your battery's in the off state.
You will have to remove a battery terminal when not running and check with a meter that is not happening.
If it is the wiring can be fudged but check first.