Entropy is an important part of the biological processes of life. A trap that "eliminates all entropy" would not just be a speed trap; it would be a literal death trap.
Barry worries that by going into the future to check on Nora in 2049 will cause another Flashpoint. However, he has it backwards; only changing the past (like saving his mother and imprisoning Thawne) would do that. Whatever causes the Godspeed army to start is in the future, so he can prevent it and keep the present unaffected.