First of all, don’t get too caught up in the warranty side of things, as most manufacturer’s warranties aren’t worth the paper they are written on (or something like that). If you look at most warranties there are several things you must do to keep it intact, and there will be several exclusions for damage by other, acts of God, etc.
Now, on to your system and your question. First, yes you will likely be bumping up the price for a built-up roof if you comply with several of the suggestions on this board. In fact, the polyisocyanurate insulation I recommended will drive the price up substantially, but you may recoup that money down the road in heating/cooling costs. However, if you are well insulated above the acoustic celing, then you may want to go with some basic insulation just to provide a suitable roofing substrate.
You say you have a fluted metal roof deck, so that tells me you need to mechanically fasten roof board insulation to the metal deck using insulation screws and stress plates. Depending on the location of your building, height, ground roughness, etc., you may or may not want to install the insulation to comply with FM (Factory Mutual) wind up-lift loss prevention guidelines. You would need to have it determined whether you should go with FM I-60, I-90 or I-120. Basically, you would probably be looking at I-60 or maybe I-90. I personally would probably opt for I-90 if you have many straight-line winds or tornadoes in the area.
Next you need to decide what type of insulation to use. Since you would be using it strictly as a substrate, and not for its R-value, I would probably opt for a nominal 1-inch thick fiberglass insulation at the minimum (I would prefer 2-layers with staggered joints), rather than organic wood fiber or perlite. The fiberglass will stand up better to moisture intrusion if you ever have leaks. Still, choice of insulation is certainly something you can value-engineer down.
Now you have to decide what type of roof membrane to use. This would also affect your insulation choice. First off, I would recommend either a built-up asphalt roof membrane or a modified bitumen roof membrane. However, you could opt for PVC, spray polyurethane foam (applied over existing roof), EPDM, or any number of membranes. I think my first choice would be a built-up roof (BUR) for your building. You could go with the modified bitumen or even a BUR with a modified bitumen cap sheet, but you probably would be fine with just a BUR. Now, you need to determine whether to go with a 3-ply system or a 4-ply. In my way of thinking, the cost for a fourth ply is not going to be that much more, and the roof system will be so much better.
Alright, so by now you should either be deciding upon a 4-ply BUR or a spray polyurethane foam roof. Once again, you would want to talk to Aaron if this is the route you want to go, and with your building it might be the best alternative. You wouldn’t have to worry about tear-off, and the foam would add reflective and insulating qualities to the roof. Anyway, if you go the BUR route, you have to decide whether to go with a glaze coat (not recommended), flood coat and gravel (provides fire rating) or emulsion and aluminum coating (possibly the best option for the money). The other option would be a 2- or 3-ply BUR with a modified bitumen cap sheet, but that would probably be too costly when compared to your other bids. At the same time, remember this roof is going to serve you for years to come and will be the most important part of the building structure.
Back to warraties for a minute. You keep mentioning Durolast’s warranty, but with a BUR system you can also get a NDL (No Dollar Limit) warranty. Depending on the BUR system and manufacturer, you can generally get 10-, 12-, 15- and 20-year warranties standard.
Okay, now lets move on. The next thing you will want to consider is flashings and counterflashings. If you go with the BUR or mod. bit. roof, I recommend modified bitumen flashings along base of walls, curbs, parapets, etc., and I recommend minimum 24 gauge prefinished (Kynar 500) galvanized/galvalume metal counterflashings that are shop fabricated.
Good luck. If you have any more questions, let me know.