test: remove fixed tests from fragile lists

Checked and found that:

  #4353 -> tarantool/tarantool-qa#13:
    engine/ddl.test.lua fixed in #6102.
  #4926, tarantool/tarantool#115:
    box/alter_limits.test.lua fixed in
    tarantool/tarantool-qa#126.
  #5547 -> tarantool/tarantool-qa#50:
    box/net.box_schema_change_gh-2666.test.lua fixed in
    tarantool/tarantool-qa#126.
  #5583 -> tarantool/tarantool-qa#22:
    box/net.box_methods_gh-3107.test.lua fixed in
    tarantool/tarantool-qa#126.

Closes tarantool/tarantool-qa#13
Closes tarantool/tarantool-qa#115
Closes #4926
Closes tarantool/tarantool-qa#50
Closes tarantool/tarantool-qa#22