Server-Side Sync Email thread tracking

I have some principle questions re. Email, appointmenst etc... sync/archiving between Outlook/Exchange and CRM, in particular Exchange 2016 (Outlook 2013+2016) and Dynamcis 365 - all on-premise.
Earlier we used Email Router + CRM for Outlook with CRM 2011. Now we are in testing phase for upgrade to Dynamics 365.
I understand that additionally to Email-Router there is another piece of software called Server-Side Sync (which I already have ocnfigured, but it does not work reliable so far, maybe becasue of my lack on understading how this is supposed to work).
CRM for Outlok is clear to me, with that one, an user can manually track items into CRM, set regarding etc. But now the automated synching (tracking) comes into the picture. I want to get Exchagne objects, mainly emails, archived/synched to CRM, which are received by an Exchange user from a CRM contact. But not each and any email from such should be archived to CRM, not just because an email is received by Exchange from crm.contact@customer.com and this email is assigned to a contact in CRM. There needs to be an initial email from this thread beeing tracked already. Because there is a lot of communication between aftersales e.g. and this customer, maybe even containing rather large log file attchments etc.. however non-sales relevant topics. And these should not be tracked, except the recipient does it manually via CRM for Outlook (and subsequent communication than will be synced too).
From what I understand from this great post http://survivingcrm.com/2014/03/synchronization-vs-tracking-understanding-activity-management-options-dynamics-crm/ is the server-side sync is supposed to cover exactly this situation, when you read this part "Why Synchronization Does Not Cover Tracking" somewhere below it states:

"Once the item is in CRM, server-side sync can take care of tracking the subsequent updates to it. A re-scheduled tracked appointment will get updated with the new date, regardless of whether you change the date via CRM or your mobile phone calendar that’s linked to Exchange. An email thread with a tracked message and a tracking token ID injected into the email subject line will have the next replies automatically synchronized into CRM."

Now I am more interested into Email-Handling, because we do not use CRM to send, receive, read or write emails as the leading system, but exclusivelly Outlook/Exchange. The reason for this is that even our sales reps do more than 50% of their Email-communication outside CRM, I mean without any logical link to any CRM item, communication between colleagues, friends, etc.
The statement above "Once the item is in CRM, server-side sync can take care of tracking the subsequent updates to it." would mean that based on my initial example, where crm.contact@customer.com sends an email to my sales rep, but this is not part of a initially tracked thread, will not be synced via server-side sync, correct? On the other hand, if my sales rep sends an email to crm.contact@customer.com and tracks it via CRM for Outlook, the response, and any other emails exchanged on the same thread, will be automatically synced? Another thing which is unclear to me is the sentence "An email thread with a tracked message and a tracking token ID injected into the email subject line will have the next replies automatically synchronized into CRM." - does that mean that this automation only works if we use Email Settings in CRM Settings with "Use tracking token" set? If we do not do so, server-side sync cannot detect such email thread objects? this wouldn't be nice, since if we are forced to use "Use tracking token" this woudl mean that on my reply the recipient wont just see the subject: "ask for a quote" but it wil look like "CRM:ask for a quote", is it?

I fear, that in order to achive what I want, I have to solely rely on manual CRM for Outlook tracking, do I?

kind regards,
Dieter Tontsch
mobileX AG