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Dealing with distortion is an art form and sometimes has to begin with the design itself.  In designs with important interface dimensions, you should consider using thicker members to allow milling the important surfaces to final dimension after welding (and pwht if it is required) is complete. Depending on how large and complex the article is, the design may have to permit shimming at assembly - this will need to be discussed with your engineer.  Sometimes you can bend the article back into position with presses or smaller spot rams. Be careful with this practice as you are probably yielding material in order to regain your dimension and drawing conformity (Always PT all welds after this practice). DO NOT HIDE THE FACT THAT YOU ARE PERFORMING PRESSING OPERATIONS FROM THE ENGINEER - THEY MUST KNOW THIS MAY BE NECESSARY AND ALSO ACCEPT IT IS A FACT OF LIFE.  The responsible engineer will then evaluate whether yielded material is detrimental to his/her structure.        Clamping to a work table may reduce some distortion; usually after your first piece you can see what the behaviour is and perhaps prior to welding you can prebend members opposite the expected directions of your distortion. Then too, your welders needs to work their heat in zones so as to avoid concentrating all the heat in one area for prolonged period. You will read in all the references that most aluminum alloys do not require preheat or may list a nominal room temperature as preheat. We have learned that preheating to about 100 degrees or above may have several weld quality benefits, including distortion control. Pay attention to interpass temps which will vary depending on alloy. These are significant for metalurgical reasons but are important for distortion concerns also.  Typical for us is about 250 deg F on 5xxx & 6xxx EXCEPT for 5456 where we have a max interpass of 150 deg F.  Beware Whitey! I am just rattling off on our shop practice, you must educate yourself on the good and bad that comes out of your own shop. 

The comment from your engineer seems typical of a Government engineer. Would that be correct? His/her idea of distortion may not be what you are thinking about. Everything will distort under load. His/her design must predict and survive the intended service as well as the flexure attendant with those service loads. The statement has no bearing on the shop welder who will build to print.   I suggest you get his butt into your shop and go over the realities and educate him/her a little. Or who knows, they may educate you as well. At any rate an exchange of information is a good thing.

Sorry fo rambling - I hope something here was useful to you.