They make decisions like that based upon practical needs. No one makes an electrolytic 0.001uf cap. In fact the whole point of electrolytics is that they make a large amount of capacitance in a small volume. You could replace them with film caps, but a 40uf 450v film cap would be HUGE. There is no point to them in small values. The polari9ty thing is to the benfit of the cap, not the circuit. The nature of electrolytics makes them polarized, unless you get specially made non-polar types. You could put plain old not polarized film caps in place of electrolytics if you could find them in sizes that fit.
SO if you have a favorite brand of film cap, great, use it. Those other forms are not film caps anyway. Ceramic discs are cheap. They worked well enough in guitar amps, but I don't recommend them for the most part. Oh the three feedback caps in the trem oscillator can be anything, and ceramics are good enough for that, there is no tone to a trem oscillator.
SMall value caps like the 250pf treble cap in the tone stack or a 100pf or whatever brightness cap can be ceramic. They are tiny and not so prone to microphonics as the large ceramics. Many people prefer to use silver-mica caps in those places. Silver micas tend to be smaller value caps. The amp only has a couple small caps, the bright caps, the treble tone stack caps, and the little 10pf cap across the 3.3M resistor where the reverb mixes. SO the added cost of silver mica should not be an issue. And really, going to s-m for those couple caps is not going to upset your original-purity approach.
The thing is really practicality driven. If you can find a 10pf film cap, go ahead and use it. Or a 250pf one. The reason Fender usede ceramics for those few and film caps for the rest is a matter of what is reasonably available or not extra costly.
A quick look at Mouser and I found for 250pf 500vcaps:
film - none
mica - $1.41 each
ceramic - 14 cents each
Adding over a dollar and a quarter to the cost of that part in each and every amp they made with that part (most of them) for the benefit of some tiny perceived tone shift was not good business.
SO make your parts list. Go down the caps and fill in each cap with a film cap if you can. Then fill in the blanks with mica or ceramic.
And for heavens sake, don;t WORRY about it. It is just a guitar amp, changing a couple film caps to mica or ceramics to film is not going to make your Fender sound like a Crate.