A fix for the problem is already available in Mate git: https://github.com/mate-desktop/mate-session-manager/pull/223. Patch is available at https://patch-diff.githubusercontent.com/raw/mate-desktop/mate-session-manager/pull/223.patch. I have tried to apply the patch to mate-session-manager 1.22.0 as well as 1.22.1, and both versions compiled successfully with the patch and the delays and dialogs went away.
@Maxim, I am willing to open a PR request for that. The thing is that it seems that no gentoo developer is willing to review PRs for the mate-project even though the official maintainers of the mate project is no longer active. See here https://github.com/gentoo/gentoo/pull/13820 and https://github.com/gentoo/gentoo/pull/13807 Both are open since early Dec. 2019. I have tried multiple times to contact the gentoo-mate devs in the IRC channel but it seems abandoned. In the meanwhile you can add my overlay[1] and enjoy updated ebuilds (both 1.22 and 1.23 series are there). [1]: https://github.com/oz123/mate-de-gentoo/
commit 6017ca56039f27024dd41e67879d6e0cc442fbe3 Author: Adam Feldman <NP-Hardass@gentoo.org> Date: Fri Mar 20 20:56:41 2020 -0400 mate-base/mate-session-manager: Bump to 1.24.0 Package-Manager: Portage-2.3.82, Repoman-2.3.18 Signed-off-by: Adam Feldman <NP-Hardass@gentoo.org> commit f0eacc97bfefac343c0ebe19cea4003cf18be7fa Author: Adam Feldman <NP-Hardass@gentoo.org> Date: Tue Mar 3 16:42:37 2020 -0500 mate-base/mate-session-manager: Bump to 1.22.3 Package-Manager: Portage-2.3.82, Repoman-2.3.18 Signed-off-by: Adam Feldman <NP-Hardass@gentoo.org>