Not sure where you are, but Theodore Robbins Ford in SoCal is mod friendly to say the least. They get warranty work done for ridiculously modded cars and trucks all of the time!!
No dealer should refuse to perform warranty work for an issue unrelated to any modifications present. The ones that do are usually in trouble for other warranty issues, which is why they are hesitant and turn work away. However, that doesn't mean that dealers will warranty an issue if it is suspected or confirmed to be caused by a modification. It's all spelled out in Ford's Warranty & Policy Manual. If the issue is suspected, but not confirmed to be the result of the modifications, the field rep will typically be involved and will make the determination as to whether the repair is warrantable. So regardless of what the dealer decides, the decision is overridden by Ford corporate.
On the other hand, there are dealers who commit warranty fraud by replacing components that were clearly damaged as a result of modifications. For example, repairing/replacing a transmission under Ford warranty due to a grenaded planetary on a Roush Supercharged 6.2 Raptor. Not warrantable in the least. It eventually catches up with them, and then they're not so "mod friendly".