On second run of seed job JobDSL recreates organizationFolders and triggers build for all jobs in it, with build cause 'Branch indexing'. SkipInitialBuildOnFirstBranchIndexing is configured in build strategies, and first run of seed job is indeed skipping builds, but second run seems to ignore that.

Are there any ways to prevent this? My understanding is that for MultiBranchPipeline it's done by 'id' parameter, but what about all mutlibranch pipelines created by organizationFolder?

Possible hack to diminish impact is to add when clause to all pipelines to skip stages on Branch Indexing, but that's way less then optimal:

when {
 not {
   triggeredBy 'BranchIndexingCause'
 }
}