Your issue is with the shop, not with PADI. Of course, there will be some others on this forum that applaud them for spending so much added time going into detail making sure you are well grounded in the material. Of course I am making assumptions on how much time you actually spent - "just as long as" doesn't tell me if you spent 1 hour, 4 hours, or something else.
I tell my eLearning EAN students to plan to spend an hour with me at the shop after they have completed it. We do the 10 question eLearning Quick Review, we discuss any questions about the course content, and I use a "show and tell" to go over some basics about EAN markings, O2 clean versus not O2 clean, VIP labels, various types of stickers and logs, use of their personal dive computer for EAN, and then do the two tank analyses. Before eLearning included the c-card in the course cost I would just collect enough to pay for the card. Now that it is included, I am happy to simply book the eLearning revenue share as compensation for the hour of my time.
Assuming it was several hours you spent in the classroom, this might be an instance of a long-time shop with a well established way of doing their thing treating eLearning as just a replacement option for the book purchase. Rather than embracing the flexibility and options allowed by eLearning, they may be resisting the convenience and making as few accommodations as possible for the technology. A similar way to describe it is that they may routinely schedule multi-student classes using traditional classroom, and just insert an infrequent eLearning student into that same class rather then tailoring an additional version solely for eLearning.
I think the most important take-away from this and similar threads, is NOT to start by purchasing the eLearning course and then look for a shop. Contact the shop first to understand their options and the way they handle eLearning, and depending on the answers decide if you need to do a little comparison.
Again, PADI shops and instructors are independent entities, not franchisees reporting to a corporate parent. Look to the front line provider with your pricing questions, not to PADI.