It sounds like you are transitioning from semi-automatic to mechanized welding. As long as the welding parameters are within the ranges qualified by the PQR, you should be fine.
Essentially you are clamping the FCAW gun to the tractor that runs on the track. The operator is still setting and monitoring the parameters of voltage, wire feed speed, travel speed, and electrode extension. The track and tractor simply guide the gun along the joint.
I would not expect the change you have proposed to have an affect on the mechanical properties provided the ranges of the welding parameters are within the ranges permitted by Table 4.5. If the ranges used in production are not within the qualified ranges, all bets are off and a new PQR will be required.
One question: if you know you will be using the mechanized method in production, why not qualify the process as mechanized to begin with and work out any bugs before backing yourself into a corner. Discovering an issue on aboard a barge can be mighty expensive and could cause a serious delay. The last thing you need is for delays and the associated costs to be attributed to you or your team. The question will be asked why all the bugs were not worked out before assembling a crew, the barge, support boat, NDE team, etc. There will be a learning curve!
Al