Ok sounds good, I am thinking I can charge a smaller cap to a higher voltage to reduce amps on the primary yet get the same energy.I am fairly certain the layout is designed per the datasheet maximum current of 10A on the primary. Even the datasheet proposed layout for the LT3750 could run into problems if you try to push it up to 20A which is probably why the LT3751 has a different layout to handle higher currents. I would recommend if using the LT3750 to simply set the primary at maximum 10A. I know you wanted 20A but I don't think it is achievable with that part. Also I would not use the LT3751 recommended 2.5uH transformer with the LT3750. Sure it may 'look' like it works in sim, but could damage parts because it is not recommended on the datasheet. The LT3751 allows lower inductances to 2.5uH but the LT3750 allows a minimum inductance for proper operation of 10uH on the primary.
You are correct to be concerned about to much current. It exceeds datasheet recommendations. I would not do it. If this circuit requires high reliability over the long run there is no guarantees after you step outside the boundaries of the datasheet.