So I wanted just little pieces of pyralux circuit board that connect all these little components together haphazardly. I wanted these little pieces laser cut and assembled (PCBA). They wanted to bill me for 5 designs but I told them it was really all 1 design just little pieces that overlay eachother and stuff. It wasn't part of many different projects like they were treating it. And they bumped the price way way way up based on 5 designs.
Is there any way to work around this? or way to explain this better or a company that would do this without saying its 5 designs?
You didn't tell us who "they" were, i.e. which company you talked to and what their quoted price was. Low-cost PCB houses like JLCPCB offer very competitive prices, also on flexible PCBs. While they also adhere to the definition "If it's multiple unconnected sections, then it's multiple designs", you may find their pricing much more affordable.
One of the reasons JLCPCB is cheap is because their process is highly automated. So you will be in charge of the CAD design, using a proper PCB layout tool -- no "painting" in some general-purpose drawing program. They have their own "EasyEDA" PCB CAD program which is available for free in ain online version.
As a general comment, I am not sure you really want to use
flexible PCBs unless you really need the ability to bend them (e.g. to use some longer traces as interconnect to other modules). They are much more sensitive than rigid PCBs, and flexing them where components are mounted will also put stress on the solder joints. You can get thinner FR4 material than the standard 1.6 mm; JLCPCB lets you go down to 0.6 mm at a small extra cost.