Ernst Mach until his death in 1916 completely denied atoms existed, as indicated by Boltzman's theories & confirmed by Einstein. Because he believed in continuous substances, and waves, as fundamental. We should be as wary of a bias toward thinking everything is made of lumps, as the converse. We don't have to make up our minds except on the basis of evidence, and until then keep our minds open. Physical intuition can be useful, like say the idea of no action-at-a-distance around since before Newton & a major source of criticism of his theory, & which principle was borne out centuries later by Einstein's work. Intuition or guiding principles can inspire, but are a poor guide if they prevent us accepting evidence, as Hossenfelder makes the case in Lost In Math.
Our best picture is not exactly of everything as particles, but everything as fields with particles as excited states of those fields. That is, Quantum Field Theory (QFT). Bosons have rest mass because they interact with the Higgs field, by the Higgs mechanism.
Water waves are distortions propagating through a bulk. Quantum waves like DeBroglie's, are matter waves, waves in the probability of a finding a particle at a given location. In the same way other fields can distort within space-time, we know space-time itself distorts. At a blackhole, the distortion becomes so strong that all the possible tracks of particles inside, even of photons, cannot cross the event horizon, making the inside causally separated from the outside (Hawking radiation involves one half of entangled pairs, so information flow out is still an issue).
We know General Relativity (GR) doesn't mesh with QFT. Canonical quantisation of relativity, works for Special Relativity. The Wheeler-DeWitt equation is the furthest towards combining GR & QFT, and it's notable it has no time variable. The disjoint between the quantum picture where time is just background & nearly everything is reversible, & GR where time is part of space-time, essentially a field, is a major problem.
What we need is a picture where space & time are not fundamental. As @nielsnielsen mentioned already Loop Quantum Gravity is one such approach.
It makes sense to step back, and look at what we know about what a dimension is. Noether's theorem tells us conservation laws are directly equivalent to continuous symmetries under transformation. So how might time be emergent?
Discussed here: How can time have a beginning when a beginning needs time?
The other concept required is the physics understanding of locality, a definition of what it means to be near or next to something. This has to do with the speed of light, and the possibility of information flow.
Distortions in space-time are in the patterns of where particles will manifest, and how information will flow. These are what we think dimensions are, or rather the emergent symmetries in these.