test: mark tests as fragile in a test's configs

Fragiled flaky tests from parallel runs to avoid
of flaky fails in regular testing:

  box-py/snapshot.test.py                ; gh-4514
  replication/misc.test.lua              ; gh-4940
  replication/skip_conflict_row.test.lua ; gh-4958
  replication-py/init_storage.test.py    ; gh-4949
  vinyl/stat.test.lua                    ; gh-4951
  xlog/checkpoint_daemon.test.lua        ; gh-4952

Part of #4953