This suggests that the spike heads are too high, preventing the string from being pressed firmly onto the fret when using the thumb, while the other fingers can be placed more precisely.

Spike location seems OK.

Check if the spikes can be driven in further while leaving enough room for the string. If not, can the spike heads be filed thinner?

The heads of the spikes need to be dressed properly.

Watching Richie Dotson install mine he carefully files them into smooth little bumps. not old toy train parts.

They wont snag a finger of interfere with fretting.

As others have implied, if properly installed they should not pose a problem to fretting with the thumb. I have had spikes in numerous banjos and never had an issue with fretting the 5th string with the thumb.

Bobby

My spikes are set for .012” for use with a .010 5th string. I can feel them when fretting the 5th, but they are low enough to not cause any problem. My vote is to see if you can go lower with them.

Hi Alex
As I write this, I have my Nechville Meteor in my hands. It's my daily practise banjo and it has spikes from frets 7 through 10. The spike heads are slightly rounded and are barely noticeable when fretting. I play mostly melodic/single string style and fret the 5th a lot. Never have any problem using thumb or finger to fret the string. I'd suggest having a luthier profile the heads of your spikes to make them more comfortable, and set them as low as possible in the fret board whilst still permitting the string to slide in and out (obviously!).

"I'm having a hard time fretting the 5th string at spiked frets if I have to fret with my thumb."

The fingertips have thickened and stiff skin from playing.  But the side edge of the thumb does not -- the skin is soft and cannot press the string down firmly enough.

Give it some time and practice to get the side edge of the thumb toughened up.

I discovered this when I had a deep splinter removed from the left side of my thumb around the knuckle and it took 3 weeks to heal.  After that, I could not get a clear note fretting the 5th string with the thumb.  Took a couple of weeks to get the thumb skin back in shape.

Hope this helps.  You'll get there.  If you can fret clearly with a finger, then the spikes are not the cause, and you'll be able to fret clearly with the thumb eventually.   I'd hold off on any work on the spikes for a month or so, see what improvement there is in fretting.