Thank you for the explanation.
Still I do not understand why:
1) If i apt-get update, package kit does not see that the package info got updated and I need to also run the pkcon refresh tool manually. Wouldn't package kit be better off by looking at package file access times? If some package lists got rewritten in the last hour, package kit should not think that the package cache had not been refreshed for, say, 11 days, should it?
2) Why should package kit think that everything had failed if it sees files having been accessed for write later than the time it thinks is the latest access time?