There's no beaker reduction, what they did was you have your base beaker amount (including all your science multipliers). That beaker amount is further multiplied by prerequisite and the % of civs that already know it bonus. You overflow the base beaker amount, not the multiplied amount, but the leftover beaker amount gets the multipliers of whatever tech you decide to choose next.
What happened before is that it kept the original multiplier from the overflowed tech and did not get the new techs multiplier. If you overflowed newly discovered liberalism to masonry, your overflow would get no multiplier whereas any new beakers to masonry would. Conversely if you overflowed masonry to starting on liberalism, you'd get the bonuses.
Binary research will for the most part have nothing to do with multipliers. It can only help if while saving up gold other civs research your tech and give you a discount.
I'll try to think of a low math example.
Dave & Buster's having a 2 for 1 cash to D&B currency sale. You buy a soda with a $100 bill and they give you change in multiplied D&B dollars. Pre 1.61, you go to their new affiliate, Bave & Dusters, who accept Dave & Buster dollars but do not have a 2 for 1 cash sale. You revel in how you have almost $200 of Bave & Dusters money for $100.
Then the management, Fireaxis, finds out about how cool, smart customers are upholding the righteous principles of capitalism and free market. After consulting the headless chicken southpark oracle, they issue decree 1.61: when customers leave Dave & Busters or Bave & Dusters, they will receive an IOU for their leftover DB dollars, but the number will be in real dollars. Customers can exchange the IOU at Dave & Busters at Bave & Dusters, and on 2 for 1 days it will get double the dollars.
If this makes sense to you, then you should see how you don't lose money from overflow, you just can't gain money.
And then the management Fireaxis decides to issue decree 3.19