I have an existing Zone 1-2 travel card (Citymapper Pass) which covers upto Boundary Zone 2
Beware that, unless things have changed since its launch,
according to this Guardian article the Citymapper Pass is not a Travelcard:
https://www.theguardian.com/uk-news/2019/feb/27/citymapper-pass-launch-london-travel-card-with-cheaper-rate-than-tfl said:
Technically, it operates as a simple pre-paid debit card, with Citymapper paying TfL for each journey its users take until they hit the standard weekly price cap.
Rather, it's a contactless debit card that Citymapper pays for, so you're actually using Pay As You Go with the card. This means that, unlike a Travelcard, it is not valid together with a Boundary Zone ticket, and you always have to touch in and out at the start and end of your journey with the card (so you can't combine it with another ticket without getting on and off the train at the splitting point).
That being said, at Stratford there should be standalone Oyster readers by the Jubilee Line platforms for you to tap in/out at when changing between train and tube, so it's not a big problem. Just something to be aware of when the Jubilee Line is disrupted, that you still have to tap in/out at Stratford and (assuming your separate ticket is valid between Rayleigh and Stratford only) won't be able to stay on the train to/from Liverpool Street, or Whitechapel once Elizabeth Line opens.
As for prices:
No splitting:
A season ticket Rayleigh to London Travelcard Zones 2-6 costs
£113.60 for a week (or £436.30 for a month which is
£100.34 per week). (I found these prices in the season ticket calculator by searching Rayleigh to Limehouse)
Including Zone 1 costs
£135.80 for a week (or £521.50 for a month, which is
£119.93 per week).
Splitting at Stratford:
Rayleigh - Stratford:
An Anytime Day Return costs £27.50, so 3 trips a week costs
£82.50.
A Flexi Season costs £192.50 for 8 trips, so 3 trips a week costs
£72.19.
A season ticket costs
£99.00 for a week (or £394.80 for a month which is
£90.80 per week).
Stratford - Canary Wharf:
Oyster/contactless Pay As You Go costs £1.70, so
£10.20 for 6 trips a week (but if you travel more then you'll be capped daily at £7.40 and then calendar-weekly at £37.00 for Z1-2 or £27.70 for Z2 or Z2-3).
A Zone 1-2 Travelcard costs
£37.00 for a week (or £142.10 for a month, which is
£32.68 per week)
A Zone 2-3 Travelcard costs
£27.70 for a week (or £106.40 for a month, which is
£24.47 per week)
A Citymapper Super Pass for Zones 1-2 costs
£33.00 per week.
You can do non-stop splits at other stations on the route, provided you combine with a proper Travelcard at the London end. According to brfares.com the Boundary Zone tickets are day returns/singles only and cost the same as tickets to the last station in the zone (Stratford, Manor Park, Goodmayes, Chadwell Heath, Harold Wood). If you're combining a Flexi Season with a Travelcard, then I think, depending on whether you want Z1+ or just Z2+, Manor Park (+Z1-3 for a total of
£107.10/week) or Goodmayes (+Z2-4 for a total of
£86.61/week) are cheapest. (I'm assuming that once you tap in with the Flexi Season in the morning to activate a ticket for the day, the ticket is valid for travel out and back without you having to tap out and in at the London end, but I could be wrong...)
(Note that some prices will increase soon.)
Thus it seems that if you only travel 3 days a week, or if your travel is irregular, then you should just combine a Flexi Season with PAYG for
£82.39 per week, as this price simply means spending £27.46 each day you travel, and wasting nothing if you don't travel (provided you use up all 8 Flexi Season trips within 28 days). If you make additional journeys within London on the days you go, then thanks to the daily cap you'll pay at most
£94.39 per week. If you regularly go to London more than 3 times a week then maybe some combination involving season tickets is better. The Citymapper Pass doesn't seem worth it unless you're paying £40/week for a Super Duper Pass and making significant use of the extra benefits, without needing any proper Travelcard benefits.