There are a couple of items that I will explain from your post. The first thing that I noticed is the Index Segment Count. By default, this setting is configured for 20. In SmarterMail 16 and earlier versions, we were using an older version of Lucene and this setting worked. In the latest versions we have upgrade Lucene indexer to the latest version and made significant optimizations throughout the product. We are going to be increasing that default number for new installs to somewhere between 1000-2000. This will positively impact your CPU by increasing that number without negatively impacting indexing. Second, at 6:37 the log states that it found 53 deletes and 2501 items to index. By default, we chunk indexing into 2500 items per "loop". After it has committed that round of indexing it will then index the next 2500, etc. At 6:38 the log states there are xxx number of unindexed items remaining. Zero items are left to index and the user is removed from the queue. I agree that it can be misleading with the quantity and percentage shown. At first glance you can expect that number to increase instead of decrease overtime to when you have 100% indexed. I will discuss this with the team and see about changing it to lessen confusion.
I hope this helps!