I just brewed a blonde ale based on a kit recipe, I tweaked it to make it my own but I followed the kit's pattern.
Kit Cost $39.89
My Ingr. $41.40
Diff = $1.60
Not much of a difference but I think its only a small price to pay to know I got my choice of hops, specialty grain, and yeast and my choice of brand. Infact if you factor in that I still have 1oz of hops leftover there's pretty much no difference.
I'm not sure why the difference though. I would have to say that logically you would think a kit cost more based on the extra processing involved, and additional packaging/marketing costs.
I'm probably not doing the kit producers justice when I say that I think you can easily take a kit recipe and sort of shadow it with your own choice of ingredients for plus/minus 10% of the kit's original cost and have the confidence of knowing you chose the ingredients. The only additional cost I can see here is bottle caps and sanitiser which for a single batch should average around $2.00 - $1.50 per batch more (based on 5gal), give or take depending on quantity discount. And don't worry it will still come conveniently packaged in a nice box, just without the colorful pictures, unless your retailer uses tie-dye shipping labels. I'm not sure about your retailer but at the online retailer I use I've compared a few recipes and found the 10% fluctuation in cost to be pretty accurate assuming your buying small quantities. If you by bulk it will be even and even more narrow variation.
In fact I think shadowing kits is an ideal way to start easing into creating you own recipes; you adjust the kit recipe and make it your own, down the line you adjust this recipe to correct for inadequacies (be there any) thus further customizing it, and before you know it your pretty much making you own original beer. That's how I plan on progressing. The experience alone IMO is worth the minor cost.