The initial smaller design will estimate the first order model with some two-factor interactions. The small number of runs does not allow some combinations of factor levels that would reduce or eliminate the correlation between the estimates (Alias Matrix).More runs would allow more combinations and increase the power of the tests for significant effects.
The second, larger design will also estimate curvature in the response to changing X2 and X3, a different model that the one proposed to the first design. The large number of runs also permitted forming combination to eliminate the correlation of the parameter estimates. This maximizes the power of the tests of significance.
Given that you don't know the response standard deviation or effect of these factors a priori. you might run an initial design, learn what you can, and, if necessary, augment the design with new runs using DOE > Augment Design. Your initial experiment can't fail, it can only disappoint you, in which case, you can improve it without starting over or quitting.