$999 is a price point that Apple always aims to place a product at (because it's 3 digits instead of 4). They'll cut corners to make it happen at the margins they want. That's why the base model ram/ssd config hasn't changed for years, and now they are now using a generation old SOC and a dated chassis.
Yes, upgrades have always been expensive, but it's worse now because they've been further optimized to funnel buyers upward. Walk in the door for a $999 MBA, add $200 for a current gen chip and modern design, $100 for the 10 core gpu, $200 for 16GB and $200 for 512GB and suddenly the $1999 14" MBP is looking like a good deal at double the price of what the buyer came in to pay.
If you can find a graph of the average selling price of macs not increasing, have at it, but I'm quite confident it has gone up. I swear they used to report this number (and it was increasing), but I'm having a lot of trouble finding it now. Average selling price is a far more relevant statistic than base price, which can be and is heavily gamed.
Tim Cook's Apple is hyper focused on extracting the most value from each individual customer, and does well at it. The profits speak for themselves.