Filament blob in chamber?

It was in about 16mm - should it push all the way through to the nozzle?

@Gareth Owen Yes. This hotend isn't what is normally referred to as an "all metal hotend". In an all metal hotend the PTFE tubing stops somewhere typically at the top of the heatsink. The filament then runs down the heatsink, through a heatbreak typically made of titanium, and into the heatblock and out the nozzle. I'm pretty sure your Prusa uses a hotend that fits this description.

In this type of hotend, which is of the same principal used in the hotends found on many budget printers (my Ender 3 Pro for example), has the PTFE go through the heatsink, through a "throat", and partially into the heatblock. The PTFE butts up against the nozzle so that the filament leaves the nozzle and goes directly into the nozzle where it melts.

The differences seen here present a couple of large contrasts outside of the immediate differences in construction. First, the PTFE has to withstand a high temperature in the design that is used on the AXIS printer. With this design you don't want to exceed 250-260C. At that point the PTFE will start to melt and give off noxious and harmful fumes. Also, it melts :). With an all metal hotend the PTFE stops near the top of the heatsink. This removes the tubing from the major source of heat and therefore is much cooler. This allows the heat block to be operated at a much higher temperature. Printing materials that require 350C is now possible. Even materials like ABS which will be in the 260-275C range will be easier.

Next, since the design takes the PTFE all the way down to the nozzle the diameter of the hole that the tube passes through has to be the same as the outside diameter of the tube. In other words, if the the tube isn't pushed all the way up to the nozzle there will be a gap due to the filament being a smaller diameter than the outside diameter of the PTFE tube. The heat will cause the filament to go past its glass transition temperature and most likely it will melt causing the blob which then will lead to a jam. In all metal hotends the diameter of the hole to the nozzle is just the width of the filament. The filament can pass all the way down through the heat block and into the nozzle because the hotend has been designed in a manner which manages heat better. The use of materials in the heatbreak like titanium allow a crazy temperature to be reached in the heat block but not transferred a large distance to cause the filament to melt all the way up the hotend.

We have this hotend which appears to be an E3D clone. I've been wondering if a "real" E3D all metal hotend can replace this one and improve the quality. It's something I've wondered but haven't really concerned myself with investigating as I still think the #1 issue is getting the printer to move each axis without issue.

So, to answer your earlier question, yes, push the PTFE tube all the way down to the nozzle. With the hotend completely disassembled I pushed the tube all the way down through the heat block midway through the threads for the nozzle. I then inserted and tightened the nozzle so that it started pushing the tube back up. I reassembled the hotend so that the coupling piece was the last piece. I pushed it down and made sure that I was always keeping pressure on the tube so that it was being forced to the nozzle. It takes a bit of force. I ended up having to reassemble once because I did end up getting about a 1mm gap between the nozzle and tube and had a blockage.