Manual way, least preferred
I agree with Chuck, other tools usually use a pin number defined in the schematic pins defined in the footprint. I get that Fusion does it different, but it's really easy to make a mistake in that totally separate popup window where you can't even see the schematics symbol or your footprint and you have to manually select each pin to pad. Hope you don't click the wrong one or accidentally select two or something 😉 And yes we always verify in design review but that's not the answer.
Auto table based, better
The manual approach is a last resort though. In other tools we just open the datasheet, and copy the pin table into excel then set all pin attributes (passive, output, I'm a clock etc, size, side of part etc). Drop that table into the tool which auto-generates an initial symbol and then I drag the pins around to be where I want. But the key thing here is I didn't spend ten minutes typing in pin names and assigning numbers. I didn't make a mistake fat fingering a pin number because it's right from the datasheet. I have it in excel in case I messed up and need to change something after import. And then like fusion I can use the IPC footprint generation tool and I have a full part.
I could see a fusion feature where you let me copy in a pin name -> pad mapping from a datasheet like that. It would still work with your flow. Maybe I could define the footprint first, copy and paste my table and get a symbol auto generated that I could then edit.
Oh and BSDL, we don't even use that as an output from our FPGA tools anymore. And you can't get it for most parts anyway so table input is much better.
SNAP & Ultra
I also agree with you that nowadays I'm going to start with Snap or Ultra first. Here though your integration is not tight enough. I think Snap has a good flow, but it always imports it into a SnapEDA library, not my organized library(s), and not with my attributes. So there's always the extra step of importing it from snap, and then manually going and setting the attributes to what we need, now open the right library, import, find the part in snap. It's slow.
Real Library flow
And I don't want to go too off topic but library management in Fusion is sorely lacking compared to other tools. We do real-part driven design, so in other tools I'll find a part on digi, arrow, mouser, etc. I drop the part number into my tool and it two clicks I've added a new resistor backed by a real part number. And then later searching, it's so easy in our other tools to quickly find a 2uF 201 cap in our database and drop it into the design. The old approach of manually dropping a generic cap and assigning it a value is for the birds 🙂 We fake it in fusion with libraries and naming conventions but I don't like it.
My continuing complaint about using Fusion Electronics professionally is it puts a lot of burden on the user and tasks that are quick and simple in other tools require me to take on too much. To the point I hate to have to add a new part in Fusion. Even to just duplicate a real resistor in our Fusion library you have to duplicated it and change four sections to get it right name, description, parameters. This takes time and it's easy to make mistakes. It's not
I will say that so far the Fusion team has been very responsive to complaints / feature request and I've seen some things I asked for actually roll out. So I do appreciate that.