1)  "Is there a reason for not doing that (bottom to first strake) fillet with the other laps?"   

Probably none other than that's how they approached asembling the first one?

When I assembled my Waterlust kit I did the panel lap 'filleting' first after tacking insides then turning the hull bottom-up. Fill(et)ing panel laps w/ thickened epoxy serves to bond adjacent panels together (adds strength) then are typically left as-is for further finishing, that is they're not going to be covered with fiberglass cloth and more epoxy.

The joint between bottom and first strake's lower edges is slightly different; you're bonding both edges together then forming a surface with that filleting that then serves as a base over which fiberglass cloth will be applied as that step is addressed during assembly.

2)  "Does warming the epoxy have any negative effect on its integrity?"

When confined to the epoxy adjacent to stitches being removed, yes it does. After all that's why heat is useful when it's deemed desirable to remove those wires.

If you use enough heat (I've had 'em glowing!) you'll see the epoxy turn to whitish dust before your eyes. That's overdoing things a bit I suspect as I've pulled 'em easily enough when they've been slightly warmed with a soldering gun's tip.

The point being the epoxy in intimate contact with stitches needs to be softened a bit before stiches can easily be extracted. What little epoxy's been involved oughtn't matter in the overall scheme of things as you'll be applying more during later operations.

Point of fact being heat - via heat gun usually - is a recommended aid to removal of epoxy mistakes because it turns even cured epoxy to somthing more akin to putty, which in that state can be scraped away then disposed of.

No one I know would trust such stuff for re-use with a build yet those surfaces, once cleaned, allowed to cool then sanded and washed of dust, should be fine for further work.

   Spclark, once again thanks for reply, but I hope you don't think  was considering reusing epoxy scraps! Seriously, I appreciate your responses and am just having some fun. 

I didn't think of using a soldering iron over the heat gun to remove the stuck wires, but then my soldering tools are on the light side and meant for electronic work. As far as removing the stubborn wires I figured out some gentle heat and twisting while pulling most times does the trick.

   I literally held a lighted match next to the end of a stubborn wire. Just do it for a couple of seconds and the wire will come out with no chance of structural damage to epoxy.

To add to my previous comment, I "tack-welded" the parts first, even though the EP manual didn't mention that. The vast majority of the wires came out with no problem, but I had to hold a match to a few stubborn ones. Then I finished epoxying the planks on top of the tack-welds.

"...I hope you don't think I was considering reusing epoxy scraps!"  

Nah, never crossed my mind. I was simply explaining how cured epoxy's affected by heat such that removal can be done when deemed necessary.

Beyond 140°F most formulations begin to lose cohesiveness, something to keep in mind when choosing paint color or arranging for boat storage w/o proper shelter from the sun.

One trick I worked out was to put two short lengths of 8 ga. solid copper wire into my soldering gun's tip sockets. Approaching a stuck stitch I'd cut one side fairly short with the other side long then touch each with those solid wire ends. Circuit's completed by the 18 ga. stitch wire which heats really quickly so almost no time is needed to pull a bunch of 'em. I admit to being a novice to S&G techniques so this was my cure for several stiches I'd buried in fillets between frames & hull panels that didn't respond to just one end being heated for removal.

I'll be more careful next time....

   Spclark, in the air force my squadron launched weather satellites and I soldered many connections with a resistive soldering iron, a somewhat more sophisticated version of your soldering gun and 8ga wire. As you figured out the method really shines by concentrating the heat where it's needed and not into/onto nearby objects. Unless of course you over do it… 

On the other hand, Andrew, you can't get much simpler than holding a match to it!