Damon tried to bring us back to the topic and I'll try to answer based on my limited experience. I have built a couple of places here, so I have (minimal) some knowledge.
Often "packaged homes" are cheaper because of several factors:
1) the pre-packaged designs are often arranged to keep construction costs low -- by doing things like centralizing the plumbing to one area of the house (i.e. bathrooms back up to each other and one bathroom is just a wall away from the kitchen, etc). See HPM's infamous '1056' (square footage, not name) for one example of this. Easy to build = cheaper.
2) the pre-packaged homes have detailed materials lists already made for them. Changing the design will require the contractor or materials supplier to recalculate the materials list and, of course, can change the cost of materials or construction cost significantly.
3) even seemingly minor changes can be significant. People think that "I just want the bathroom on this side of the room instead of the other side" is not a big change, but that can have HUGE implications on cost. I've seen cases where something like "lets put this exact house up on post-and-pier rather than slab so I can park underneath" was a $50,000 change. In that case, the rules for fire-retardant materials necessary, beam changes for proper support and addition of a staircase from the carport to the main house dramatically affected the plans and cost. In this example, beams shorted by the addition of the "hole" for the staircase were important load-bearing beams and when shortened, had to be of greater thickness and strength. Higher cost, too.
Changing a "packaged home" plans can have a lot of costs beyond just new draftsman plans and a new review/approval by an architect.
All that being said, "yes, of course you have input and can make changes." Just be sure that as you discuss the changes, you are working with someone REALLY knowledgeable about the implications of the changes and how it can affect your costs. I would recommend discussing them with your contractor or experienced architect/draftsperson before you commit to the changes. Sometimes the architect is expensive and a draftsperson could answer your questions and advise you on the implications of a change for far less cost -- the architect will still have to review and approve it in the end, though.
John Dirgo, R, ABR, e-PRO
Aloha Coast Realty, LLC
808-987-9243 cell
http://www.alohacoastrealty.com