This is a consequence of. That modification moved calculation of the tax-exclusive subtotal line-item into a line-item 'display' call (instead of a 'load' call). I'm assuming this was intended to make sure that all other line-items had been loaded before calculating this one. However, as a result, this line item is no longer alterable via hook_line_item_alter(). This breaks compatibility with uc_coupon, which had to alter the pretax subtotal when dealing with tax-inclusive prices (for reasons too complicated to go into here).
This patch (which I'll attach as soon as I get an issue number) is a slight modification to the way uc_line_item_tax_subtotal() calculates its value. Instead of summing all the line items which aren't taxes, it sums all the taxes, and then subtracts that amount from the result of uc_order_get_total(). The order total as calculated by that function IS alterable (in fact, uc_coupon is already altering it) - so this resolves the problem as far as uc_coupon is concerned.
Marking this as "major" because uc_coupon is currently the only discount system ported to D7, and it would be a shame for a new release of ubercart to break it.