You can remove the plunger and trowel peanut butter thick mixes into the syringe. After doing that, you may reconsider your objections to the plastic bag method! -hah.

The bag is my preference when neatness counts. (But mostly I just flop my thick mix onto a cardboard scrap and use a squeegee to scoop dollops from- like a brick mason with mortar, on a smaller scale...)

Use a freezer bag, not a thin sandwich bag. Roll a cuff into the top before you start your batch, get your mix good and thick in the stir cup, then trowel the goop into the upright bag. Your gloved hands can stay clean for all of this. Unroll the bag cuff and seal the ziploc, then gently squeegee the mix toward a bottom bag corner. Twist the empty part like a pastry bag. Cut or snip about a 3/16 to 1/4" opening, and start laying down beads of non-sag epoxy. When you've pushed out about 2/3 of the bag, it's usually good to lay the bag on the bench and re-squeegee the mix toward your nozzle. Do try to get the joints filled all at once and without delay- don't lay down a head, tool it, and start a new bead. The wad of bagged epoxy will exotherm much more quickly do to your hand contact and being in a concentrated ball. Get it spread out as beads in your seams all at once, then lay the empty-ish bag flat on the bench while you go shape the epoxy joints. The near-empty bag will keep a little if you need some touch up material to fix a low joint.

Just did all the planks on a Northeaster Dory build and the first bag had the mixture at "mustard" per the cell-o-fill guidelines from CLC. That wound up running into the stitch gaps over the copper wires, so I increased the thickness in subsequent bags to peanut butter consistency and it was much easier to control.  I used pastry bags, but ziplock freezer work fine too. My wife just happened to have some plastic pastry bags. Anyway, they are plenty neat and don't create a mess if the stuff inside is thick enough. Two small tips: 1. once it's in the bag, hold the top closed and do a full arm spin to compress it all into the tip before you cut it open, and 2. once it's in the bag and at the bottom, twist the top of the bag a handful of times, bend over the twist and put a rubber band tightly around it. This last step stops the epoxy from oozing above your hands and out the top. 

   Thanks to both of you for all the information.  Seems strange that CLC recommends such a runny epoxy consistency that just flows out the ends of the joint. The manual doesn't say anything about working the epoxy in that joint. I have ended up with quite a few joints in which the epoxy is concave. Do I want to be filling that back in so that it's more like perpendicular to the face of the plank?  Seems like a fine line between filling the joint and beginning to bury the copper in the epoxy.  
 

I think people have different types of mustard.

On the NED, the epoxy is a bit concave into the gap, but it's still high enough that the tips of the epoxy are at the top of the slat. Ultimately it's getting the epoxy all the way into the slat for the most surface area that matters I suspect. In my ill fated first batch where the epoxy ran down the gap into the stitches, I just added more on top in the next batch to even out the entire slat gap. 

On our PMD build, we got ours thick enough to work into the plank laps with squeegees and such, mostly.  We still ended up with a few "stalactites" where the seams weren't as snug here and there.  Mostly cleaned up with a sharp chisel.

.....Michael

With regard to syringes/zip lock bags.freezer bags to squeeze out thickened epoxy, I use piping bags that cake makers use.

These are thick polythene, triangular shaped and designed for pretty much the same application when icing or decorating cakes. I only went looking for a few (this was back in 2016) and found them but in a roll of 72. They cost me 14 Turkish Lira the equivalent of $3 at the time. I still have plenty left and for me they top every other suggestion. Cut of any size piece you want from the already tapered end and make decent fillets or fill small gaps.