Currently the query killer looks for queries that have been running for longer than 60 seconds. However, the MediaWiki wall clock timeout is also 60 seconds, so if a query takes >= 60 seconds to run, MediaWiki will give up before the user gets the response.
Lowering it to 55 seconds is conservative proposal, but should be seen as just the first step. If 55s goes well, we can wait a bit and then lower it again, and repeat, until we're at a level we're comfortable with, both on the user side and SRE side.
Additionally, having metrics about this will help gauge the impact of this change (T293531: Monitor/dashboard number of queries killed by the automatic query killer).