1) Yes, tailed chicks can have tuffs.
2) Cleanface can't throw tuffs. Needs 1 parent single or double tuff to pass off for tuff gene.
3

Like any poultry, select adult birds that meet the SOP for the breed. Keep offsprings that have longer backs for consistency. Or introduce longer backs to shorter backs to improve offspring. When making decisions about your keepers, overall body type should be a priority. Things like comb and eye color are easier to improve. Type should always triumph.
Lastly, you can always vent trim or do artificial insemination to improve fertility.
Araucanas SOP is one of the most messed up SOP. Because of it, many people give up as it is impossible to adhere to.