It will depend on the capacity of the battery bank that is being used to start the engine. A well charged bank that has enough oomph to start the engine should not cause any issue with the charger. At worse it might increase the draw on the charge for a few seconds and blow the fuse. That won't be an issue if the charger is fused properly at the battery connection.
To avoid conflicts between the Alternator, Charger, and solar, have each one set at a slightly different bulk charge voltage. The primary source, the most used source should be at the highest voltage, the least used or weakest should be the lowest. The devices with the lower voltage set points will not charge when a higher voltage device is charging. So, if the charger is set at 14.9 v and the alternator at 14.8, when the engine is started the alternator regulator will see a voltage of 14.9 and ramp down the alternator output. Of course this only works if you can program the charger and the alternator regulator.